Muscle targeting complexes and uses thereof for treating facioscapulohumeral muscular dystrophy

ABSTRACT

Aspects of the disclosure relate to complexes comprising a muscle-targeting agent covalently linked to a molecular payload. In some embodiments, the muscle-targeting agent specifically binds to an internalizing cell surface receptor on muscle cells. In some embodiments, the molecular payload inhibits expression or activity of DUX4. In some embodiments, the molecular payload is an oligonucleotide, such as an antisense oligonucleotide or RNAi oligonucleotide.

RELATED APPLICATIONS

This application claims the benefit of the filing date of U.S.Provisional Application No. 62/713,933, entitled “MUSCLE TARGETINGCOMPLEXES AND USES THEREOF FOR TREATING FACIOSCAPULOHUMERAL MUSCULARDYSTROPHY”, filed Aug. 2, 2018; the contents of which is incorporatedherein by reference in its entirety.

FIELD OF THE INVENTION

The present application relates to targeting complexes for deliveringmolecular payloads (e.g., oligonucleotides) to cells and uses thereof,particularly uses relating to treatment of disease.

REFERENCE TO THE SEQUENCE LISTING

The present application is being filed along with a Sequence Listing inelectronic format. The Sequence Listing is provided as a file entitledD082470001W000-SEQ.txt created on Jul. 31, 2019 which is 60 kilobytes insize. The information in electronic format of the sequence listing isincorporated herein by reference in its entirety.

BACKGROUND OF INVENTION

Muscular dystrophies (MDs) are a group of diseases characterized by theprogressive weakness and loss of muscle mass. These diseases are causedby mutations in genes which encode proteins needed to form healthymuscle tissue. Facioscapulohumeral muscular dystrophy (FSHD) is adominantly inherited type of MD which primarily affects muscles of theface, shoulder blades, and upper arms. Other symptoms of FSHD includeabdominal muscle weakness, retinal abnormalities, hearing loss, andjoint pain and inflammation. FSHD is the most prevalent of the ninetypes of MD affecting both adults and children, with a worldwideincidence of about 1 in 8,300 people. FSHD is caused by aberrantproduction of double homeobox 4 (DUX4), a protein whose function isunknown. The DUX4 gene, which encodes the DUX4 protein, is located inthe D4Z4 repeat region on chromosome 4 and is typically expressed onlyin fetal development, after which it is repressed by hypermethylation ofthe D4Z4 repeats which surround and compact the DUX4 gene. Two types ofFSHD, Type 1 and Type 2 have been described. Type 1, which accounts forabout 95% of cases, is associated with deletions of D4Z4 repeats onchromosome 4. Unaffected individuals generally have more than 10 repeatsarrayed in the subtelomeric region of chromosome 4, whereas the mostcommon form of FSHD (FSHD1) is caused by a contraction of the array tofewer than 10 repeats, associated with decreased epigenetic repressionand variegated expression of DUX4 in skeletal muscle. Type 2 FSHD, whichaccounts for about 5% of cases, is associated with mutations of theSMCHD1 gene on chromosome 18. Besides supportive care and treatments toaddress the symptoms of the disease, there are no effective therapiesfor FSHD.

SUMMARY OF INVENTION

According to some aspects, the disclosure provides complexes that targetmuscle cells for purposes of delivering molecular payloads to thosecells. In some embodiments, complexes provided herein are particularlyuseful for delivering molecular payloads that inhibit the expression oractivity of DUX4, e.g., in a subject having or suspected of havingFacioscapulohumeral muscular dystrophy (FSHD). Accordingly, in someembodiments, complexes provided herein comprise muscle-targeting agents(e.g., muscle targeting antibodies) that specifically bind to receptorson the surface of muscle cells for purposes of delivering molecularpayloads to the muscle cells. In some embodiments, the complexes aretaken up into the cells via a receptor mediated internalization,following which the molecular payload may be released to perform afunction inside the cells. For example, complexes engineered to deliveroligonucleotides may release the oligonucleotides such that theoligonucleotides can inhibit DUX4 gene expression in the muscle cells.In some embodiments, the oligonucleotides are released by endosomalcleavage of covalent linkers connecting oligonucleotides andmuscle-targeting agents of the complexes.

Some aspects of the disclosure comprise a complex comprising amuscle-targeting agent covalently linked to a molecular payloadconfigured for inhibiting expression or activity of DUX4, wherein themuscle-targeting agent specifically binds to an internalizing cellsurface receptor on muscle cells.

In some embodiments, the muscle-targeting agent is a muscle-targetingantibody. In some embodiments, a muscle-targeting antibody is anantibody that specifically binds to an extracellular epitope of atransferrin receptor (e.g., an epitope of the apical domain of thetransferrin receptor). A muscle-targeting antibody may specificallybinds to an epitope of a sequence in the range of C89 to F760 of SEQ IDNO: 1-3. In some embodiments, the equilibrium dissociation constant (Kd)of binding of a muscle-targeting antibody to a transferrin receptor isin a range from 10⁻¹¹M to 10⁻⁶ M.

In some embodiments, a muscle-targeting antibody of a complex competesfor specific binding to an epitope of a transferrin receptor with anantibody listed in Table 1 (e.g., competes for specific binding to anepitope of a transferrin receptor with an Kd of less than or equal to10⁻⁶ M, e.g., in a range of 10⁻¹¹ M to 10⁻⁶ M).

In some embodiments, a muscle-targeting antibody of a complex does notspecifically bind to the transferrin binding site of a transferrinreceptor and/or does not inhibit binding of transferrin to a transferrinreceptor. In some embodiments, a muscle-targeting antibody of a complexis cross-reactive with extracellular epitopes of two or more of a human,non-human primate and rodent transferrin receptor. In some embodiments,a muscle-targeting antibody of a complex is configured to promotetransferrin receptor mediated internalization of the molecular payloadinto a muscle cell.

A muscle-targeting antibody (e.g., muscle-targeting antibody is anantibody that specifically binds to an extracellular epitope of atransferrin receptor) is a chimeric antibody, wherein optionally thechimeric antibody is a humanized monoclonal antibody. A muscle-targetingantibody may be in the form of a ScFv, Fab fragment, Fab′ fragment,F(ab′)₂ fragment, or Fv fragment.

In some embodiments, a molecular payload of a complex is anoligonucleotide (e.g., an oligonucleotide that targets DUX4). In someembodiments, an oligonucleotide comprises at least 15 consecutivenucleotides of SEQ ID NO: 45. In some embodiments, an oligonucleotidecomprises SEQ ID NO: 45. In some embodiments, an oligonucleotidecomprises a sequence that is complementary to at least 15 consecutivenucleotides of SEQ ID NO: 46.

In some embodiments, an oligonucleotide comprises a region ofcomplementarity to a DUX4 gene. In some embodiments, an oligonucleotidecomprises an antisense strand that hybridizes, in a cell, with awild-type DUX4 mRNA transcript encoded by the allele. In someembodiments, an oligonucleotide comprises an antisense strand thathybridizes, in a cell, with a mutant DUX4 mRNA transcript encoded by theallele. An oligonucleotide may comprise a strand complementary to thecoding sequence of DUX4.

In some embodiments, an oligonucleotide comprises a strand complementaryto the non-coding sequence of DUX4. In some embodiments, anoligonucleotide may comprise a strand complementary to a 5′ or 3′ UTRsequence of DUX4. In some embodiments, an oligonucleotide mediatesepigenetic silencing of DUX4.

An oligonucleotide of the disclosure may comprise at least one modifiedinternucleotide linkage (e.g., a phosphorothioate linkage). In someembodiments, an oligonucleotide comprises phosphorothioate linkages inthe Rp stereochemical conformation and in the Sp stereochemicalconformation. In some embodiments, an oligonucleotide comprisesphosphorothioate linkages that are all in the Rp stereochemicalconformation. In other embodiments, an oligonucleotide comprisesphosphorothioate linkages that are all in the Sp stereochemicalconformation.

An oligonucleotide of the disclosure may comprise one or more modifiednucleotides (e.g., 2′-modified nucleotides). In some embodiments, amodified nucleotide is a 2′-O-methyl, 2′-fluoro (2′-F),2′-O-methoxyethyl (2′-MOE), or 2′, 4′-bridged nucleotide. In someembodiments, a modified nucleotides is a bridged nucleotide (e.g.,selected from: 2′,4′-constrained 2′-O-ethyl (cEt) and locked nucleicacid (LNA) nucleotides).

In some embodiments, an oligonucleotide is a gapmer oligonucleotide thatdirects RNAse H-mediated cleavage of the DUX4 mRNA transcript in a cell.A gapmer oligonucleotide may comprise a central portion of 5 to 15deoxyribonucleotides flanked by wings of 2 to 8 modified nucleotides(e.g., 2′-modified nucleotides).

In some embodiments, an oligonucleotide is a mixmer oligonucleotide(e.g., a mixmer oligonucleotide inhibits translation of a DUX4 mRNAtranscript). A mixmer oligonucleotide may comprise two or more different2′ modified nucleotides.

In some embodiments, an oligonucleotide is an RNAi oligonucleotide thatpromotes RNAi-mediated cleavage of the DUX4 mRNA transcript. An RNAioligonucleotide may be a double-stranded oligonucleotide of 19 to 25nucleotides in length. In some embodiments, an RNAi oligonucleotidecomprises at least one 2′ modified nucleotide.

In some embodiments, an oligonucleotide comprises a guide sequence for agenome editing nuclease.

In some embodiments, an oligonucleotide is a phosphorodiamiditemorpholino oligomer (PMO).

In other embodiments, a molecular payload is a polypeptide (e.g., apolypeptide that inhibits DUX4 expression). In some embodiments, amolecular payload is a polypeptide that binds to a DUX4 enhancersequence, thereby blocking recruitment of one or more activators of DUX4expression.

In some embodiments, a muscle-targeting agent is covalently linked to amolecular payload via a cleavable linker (e.g., a protease-sensitivelinker, pH-sensitive linker, or glutathione-sensitive linker). Aprotease-sensitive linker may comprise a sequence cleavable by alysosomal protease and/or an endosomal protease. In some embodiments, aprotease-sensitive linker comprises a valine-citrulline dipeptidesequence. A pH-sensitive linker may be cleaved at a pH in a range of 4to 6.

In some embodiments, a muscle-targeting agent is covalently linked to amolecular payload via a non-cleavable linker (e.g., an alkane linker).

In some embodiments, a muscle-targeting antibody comprises a non-naturalamino acid to which an oligonucleotide can be covalently linked. In someembodiments, a muscle-targeting antibody is covalently linked to anoligonucleotide via conjugation to a lysine residue or a cysteineresidue of the antibody. In some embodiments, an oligonucleotide isconjugated to a cysteine residue of the antibody via amaleimide-containing linker, optionally wherein the maleimide-containinglinker comprises a maleimidocaproyl or maleimidomethylcyclohexane-1-carboxylate group.

In some embodiments, a muscle-targeting antibody is a glycosylatedantibody that comprises at least one sugar moiety to which aoligonucleotide is covalently linked. In some embodiments, aglycosylated antibody that comprises at least one sugar moiety that is abranched mannose. In some embodiments, a muscle-targeting antibody is aglycosylated antibody that comprises one to four sugar moieties each ofwhich is covalently linked to a separate oligonucleotide. In someembodiments, a muscle-targeting antibody is a fully-glycosylatedantibody or a partially-glycosylated antibody. A partially-glycosylatedantibody may be produced via chemical or enzymatic means. In someembodiments, a partially-glycosylated antibody is produced in a cellthat is deficient for an enzyme in the N- or O-glycosylation pathway.

Some aspects of the disclosure comprise a method of delivering anmolecular payload to a cell expressing transferrin receptor, the methodcomprising contacting the cell with a complex comprising amuscle-targeting agent covalently linked to a molecular payloadconfigured for inhibiting expression or activity of DUX4.

Some aspects of the disclosure comprise a method of inhibitingexpression or activity of DUX4 in a cell, the method comprisingcontacting the cell with a complex comprising a muscle-targeting agentcovalently linked to a molecular payload configured for inhibitingexpression or activity of DUX4 in an amount effective for promotinginternalization of the molecular payload to the cell. In someembodiments, the cell is in vitro. In some embodiments, the cell is in asubject. In some embodiments, the subject is a human.

Some aspects of the disclosure comprise a method of treating a subjecthaving one or more deletions of a D4Z4 repeat in chromosome 4 that isassociated with facioscapulohumeral muscular dystrophy, the methodcomprising administering to the subject an effective amount of a complexcomprising a muscle-targeting agent covalently linked to a molecularpayload configured for inhibiting expression or activity of DUX4. Insome embodiments, the subject has 10 or fewer D4Z4 repeats (e.g., thesubject has 9, 8, 7, 6, 5, 4, 3, 2, or 1 D4Z4 repeats). In someembodiments, the subject has no D4Z4 repeats.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 depicts a non-limiting schematic showing the effect oftransfecting cells with an siRNA.

FIG. 2 depicts a non-limiting schematic showing the activity of a muscletargeting complex comprising an siRNA.

FIGS. 3A-3B depict non-limiting schematics showing the activity of amuscle targeting complex comprising an siRNA in mouse muscle tissues(gastrocnemius and heart) in vivo, relative to control experiments. (N=4C57BL/6 WT mice)

FIGS. 4A-4E depict non-limiting schematics showing the tissueselectivity of a muscle targeting complex comprising an siRNA.

FIG. 5 depicts a non-limiting schematic showing the expression levels ofDUX4 in three DUX4-expressing cell lines (A549, U-2 OS, and HepG2 celllines) and immortalized skeletal muscle myoblasts (SkMC).

FIG. 6 depicts non-limiting schematics showing the ability of aphosphorodiamidate morpholino oligomer (PMO) version of an antisenseoligonucleotide that targets DUX4 (FM10 PMO) to reduce expression levelsof downstream DUX4 genes (ZSCAN1, MBDL3L2, TRIM43).

DETAILED DESCRIPTION OF INVENTION

Aspects of the disclosure relate to a recognition that while certainmolecular payloads (e.g., oligonucleotides, peptides, small molecules)can have beneficial effects in muscle cells, it has proven challengingto effectively target such cells. As described herein, the presentdisclosure provides complexes comprising muscle-targeting agentscovalently linked to molecular payloads in order to overcome suchchallenges. In some embodiments, the complexes are particularly usefulfor delivering molecular payloads that inhibit the expression oractivity of target genes in muscle cells, e.g., in a subject having orsuspected of having a rare muscle disease. For example, in someembodiments, complexes are provided for targeting a DUX4 to treatsubjects having FSHD. In some embodiments, complexes provided hereincomprise oligonucleotides that inhibit expression of DUX4 in a subjectthat has one or more D4Z4 repeat deletions on chromosome 4. In someembodiments, complexes provided herein comprise molecular payloads suchas guide molecules (e.g., guide RNAs) that are capable of targetingnucleic acid programmable nucleases (e.g., Cas9) to a DUX4 gene in orderto inactivate the gene in muscle cells, for example, by removing aportion of the DUX4 gene, or by introducing an inactivating mutation orstop codon into the DUX4 gene. In some embodiments, such nucleicprogrammable nucleases could be used to inactivate DUX4 that isaberrantly expressed in muscle cells.

Further aspects of the disclosure, including a description of definedterms, are provided below.

I. Definitions

Administering: As used herein, the terms “administering” or“administration” means to provide a complex to a subject in a mannerthat is physiologically and/or pharmacologically useful (e.g., to treata condition in the subject).

Approximately: As used herein, the term “approximately” or “about,” asapplied to one or more values of interest, refers to a value that issimilar to a stated reference value. In certain embodiments, the term“approximately” or “about” refers to a range of values that fall within15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, orless in either direction (greater than or less than) of the statedreference value unless otherwise stated or otherwise evident from thecontext (except where such number would exceed 100% of a possiblevalue).

Antibody: As used herein, the term “antibody” refers to a polypeptidethat includes at least one immunoglobulin variable domain or at leastone antigenic determinant, e.g., paratope that specifically binds to anantigen. In some embodiments, an antibody is a full-length antibody. Insome embodiments, an antibody is a chimeric antibody. In someembodiments, an antibody is a humanized antibody. However, in someembodiments, an antibody is a Fab fragment, a F(ab′)2 fragment, a Fvfragment or a scFv fragment. In some embodiments, an antibody is ananobody derived from a camelid antibody or a nanobody derived fromshark antibody. In some embodiments, an antibody is a diabody. In someembodiments, an antibody comprises a framework having a human germlinesequence. In another embodiment, an antibody comprises a heavy chainconstant domain selected from the group consisting of IgG, IgG1, IgG2,IgG2A, IgG2B, IgG2C, IgG3, IgG4, IgA1, IgA2, IgD, IgM, and IgE constantdomains. In some embodiments, an antibody comprises a heavy (H) chainvariable region (abbreviated herein as VH), and/or a light (L) chainvariable region (abbreviated herein as VL). In some embodiments, anantibody comprises a constant domain, e.g., an Fc region. Animmunoglobulin constant domain refers to a heavy or light chain constantdomain. Human IgG heavy chain and light chain constant domain amino acidsequences and their functional variations are known. With respect to theheavy chain, in some embodiments, the heavy chain of an antibodydescribed herein can be an alpha (α), delta (Δ), epsilon (ε), gamma (γ)or mu (μ) heavy chain. In some embodiments, the heavy chain of anantibody described herein can comprise a human alpha (α), delta (Δ),epsilon (ε), gamma (γ) or mu (μ) heavy chain. In a particularembodiment, an antibody described herein comprises a human gamma 1 CH1,CH2, and/or CH3 domain. In some embodiments, the amino acid sequence ofthe VH domain comprises the amino acid sequence of a human gamma (γ)heavy chain constant region, such as any known in the art. Non-limitingexamples of human constant region sequences have been described in theart, e.g., see U.S. Pat. No. 5,693,780 and Kabat E A et al., (1991)supra. In some embodiments, the VH domain comprises an amino acidsequence that is at least 70%, 75%, 80%, 85%, 90%, 95%, 98%, or at least99% identical to any of the variable chain constant regions providedherein. In some embodiments, an antibody is modified, e.g., modified viaglycosylation, phosphorylation, sumoylation, and/or methylation. In someembodiments, an antibody is a glycosylated antibody, which is conjugatedto one or more sugar or carbohydrate molecules. In some embodiments, theone or more sugar or carbohydrate molecule are conjugated to theantibody via N-glycosylation, O-glycosylation, C-glycosylation,glypiation (GPI anchor attachment), and/or phosphoglycosylation. In someembodiments, the one or more sugar or carbohydrate molecule aremonosaccharides, disaccharides, oligosaccharides, or glycans. In someembodiments, the one or more sugar or carbohydrate molecule is abranched oligosaccharide or a branched glycan. In some embodiments, theone or more sugar or carbohydrate molecule includes a mannose unit, aglucose unit, an N-acetylglucosamine unit, an N-acetylgalactosamineunit, a galactose unit, a fucose unit, or a phospholipid unit. In someembodiments, an antibody is a construct that comprises a polypeptidecomprising one or more antigen binding fragments of the disclosurelinked to a linker polypeptide or an immunoglobulin constant domain.Linker polypeptides comprise two or more amino acid residues joined bypeptide bonds and are used to link one or more antigen binding portions.Examples of linker polypeptides have been reported (see e.g., Holliger,P., et al. (1993) Proc. Natl. Acad. Sci. USA 90:6444-6448; Poljak, R.J., et al. (1994) Structure 2:1121-1123). Still further, an antibody maybe part of a larger immunoadhesion molecule, formed by covalent ornoncovalent association of the antibody or antibody portion with one ormore other proteins or peptides. Examples of such immunoadhesionmolecules include use of the streptavidin core region to make atetrameric scFv molecule (Kipriyanov, S. M., et al. (1995) HumanAntibodies and Hybridomas 6:93-101) and use of a cysteine residue, amarker peptide and a C-terminal polyhistidine tag to make bivalent andbiotinylated scFv molecules (Kipriyanov, S. M., et al. (1994) Mol.Immunol. 31:1047-1058).

CDR: As used herein, the term “CDR” refers to the complementaritydetermining region within antibody variable sequences. There are threeCDRs in each of the variable regions of the heavy chain and the lightchain, which are designated CDR1, CDR2 and CDR3, for each of thevariable regions. The term “CDR set” as used herein refers to a group ofthree CDRs that occur in a single variable region capable of binding theantigen. The exact boundaries of these CDRs have been defineddifferently according to different systems. The system described byKabat (Kabat et al., Sequences of Proteins of Immunological Interest(National Institutes of Health, Bethesda, Md. (1987) and (1991)) notonly provides an unambiguous residue numbering system applicable to anyvariable region of an antibody, but also provides precise residueboundaries defining the three CDRs. These CDRs may be referred to asKabat CDRs. Sub-portions of CDRs may be designated as L1, L2 and L3 orH1, H2 and H3 where the “L” and the “H” designates the light chain andthe heavy chains regions, respectively. These regions may be referred toas Chothia CDRs, which have boundaries that overlap with Kabat CDRs.Other boundaries defining CDRs overlapping with the Kabat CDRs have beendescribed by Padlan (FASEB J. 9:133-139 (1995)) and MacCallum (J MolBiol 262(5):732-45 (1996)). Still other CDR boundary definitions may notstrictly follow one of the above systems, but will nonetheless overlapwith the Kabat CDRs, although they may be shortened or lengthened inlight of prediction or experimental findings that particular residues orgroups of residues or even entire CDRs do not significantly impactantigen binding. The methods used herein may utilize CDRs definedaccording to any of these systems, although preferred embodiments useKabat or Chothia defined CDRs.

CDR-grafted antibody: The term “CDR-grafted antibody” refers toantibodies which comprise heavy and light chain variable regionsequences from one species but in which the sequences of one or more ofthe CDR regions of VH and/or VL are replaced with CDR sequences ofanother species, such as antibodies having murine heavy and light chainvariable regions in which one or more of the murine CDRs (e.g., CDR3)has been replaced with human CDR sequences.

Chimeric antibody: The term “chimeric antibody” refers to antibodieswhich comprise heavy and light chain variable region sequences from onespecies and constant region sequences from another species, such asantibodies having murine heavy and light chain variable regions linkedto human constant regions.

Complementary: As used herein, the term “complementary” refers to thecapacity for precise pairing between two nucleotides or two sets ofnucleotides. In particular, complementary is a term that characterizesan extent of hydrogen bond pairing that brings about binding between twonucleotides or two sets of nucleotides. For example, if a base at oneposition of an oligonucleotide is capable of hydrogen bonding with abase at the corresponding position of a target nucleic acid (e.g., anmRNA), then the bases are considered to be complementary to each otherat that position. Base pairings may include both canonical Watson-Crickbase pairing and non-Watson-Crick base pairing (e.g., Wobble basepairing and Hoogsteen base pairing). For example, in some embodiments,for complementary base pairings, adenosine-type bases (A) arecomplementary to thymidine-type bases (T) or uracil-type bases (U), thatcytosine-type bases (C) are complementary to guanosine-type bases (G),and that universal bases such as 3-nitropyrrole or 5-nitroindole canhybridize to and are considered complementary to any A, C, U, or T.Inosine (I) has also been considered in the art to be a universal baseand is considered complementary to any A, C, U or T.

Conservative amino acid substitution: As used herein, a “conservativeamino acid substitution” refers to an amino acid substitution that doesnot alter the relative charge or size characteristics of the protein inwhich the amino acid substitution is made. Variants can be preparedaccording to methods for altering polypeptide sequence known to one ofordinary skill in the art such as are found in references which compilesuch methods, e.g. Molecular Cloning: A Laboratory Manual, J. Sambrook,et al., eds., Fourth Edition, Cold Spring Harbor Laboratory Press, ColdSpring Harbor, N.Y., 2012, or Current Protocols in Molecular Biology, F.M. Ausubel, et al., eds., John Wiley & Sons, Inc., New York.Conservative substitutions of amino acids include substitutions madeamongst amino acids within the following groups: (a) M, I, L, V; (b) F,Y, W; (c) K, R, H; (d) A, G; (e) S, T; (f) Q, N; and (g) E, D.

Covalently linked: As used herein, the term “covalently linked” refersto a characteristic of two or more molecules being linked together viaat least one covalent bond. In some embodiments, two molecules can becovalently linked together by a single bond, e.g., a disulfide bond ordisulfide bridge, that serves as a linker between the molecules.However, in some embodiments, two or more molecules can be covalentlylinked together via a molecule that serves as a linker that joins thetwo or more molecules together through multiple covalent bonds. In someembodiments, a linker may be a cleavable linker. However, in someembodiments, a linker may be a non-cleavable linker.

Cross-reactive: As used herein and in the context of a targeting agent(e.g., antibody), the term “cross-reactive,” refers to a property of theagent being capable of specifically binding to more than one antigen ofa similar type or class (e.g., antigens of multiple homologs, paralogs,or orthologs) with similar affinity or avidity. For example, in someembodiments, an antibody that is cross-reactive against human andnon-human primate antigens of a similar type or class (e.g., a humantransferrin receptor and non-human primate transferring receptor) iscapable of binding to the human antigen and non-human primate antigenswith a similar affinity or avidity. In some embodiments, an antibody iscross-reactive against a human antigen and a rodent antigen of a similartype or class. In some embodiments, an antibody is cross-reactiveagainst a rodent antigen and a non-human primate antigen of a similartype or class. In some embodiments, an antibody is cross-reactiveagainst a human antigen, a non-human primate antigen, and a rodentantigen of a similar type or class.

DUX4: As used herein, the term “DUX4” refers to a gene that encodesdouble homeobox 4, a protein which is generally expressed during fetaldevelopment and in the testes of adult males. In some embodiments, DUX4may be a human (Gene ID: 100288687), non-human primate (e.g., Gene ID:750891, Gene ID: 100405864), or rodent gene (e.g., Gene ID: 306226). Inhumans, expression of the DUX4 gene outside of fetal development and thetestes is associated with facioscapulohumeral muscular dystrophy. Inaddition, multiple human transcript variants (e.g., as annotated underGenBank RefSeq Accession Numbers: NM_001293798.2, NM_001306068.2,NM_001363820.1) have been characterized that encode different proteinisoforms.

Facioscapulohumeral muscular dystrophy (FSHD): As used herein, the term“facioscapulohumeral muscular dystrophy (FSHD)” refers to a geneticdisease caused by mutations in the DUX4 gene or SMCHD1 gene that ischaracterized by muscle mass loss and muscle atrophy, primarily in themuscles of the face, shoulder blades, and upper arms. Two types of thedisease, Type 1 and Type 2, have been described. Type I is associatedwith deletions in D4Z4 repeat regions on chromosome 4 which contain theDUX4 gene. Type 2 is associated with mutations in the SMCHD1 gene. BothType 1 and Type 2 FSHD are characterized by aberrant production of theDUX4 protein after fetal development outside of the testes.Facioscapulohumeral dystrophy, the genetic basis for the disease, andrelated symptoms are described in the art (see, e.g. Campbell, A. E., etal., “Facioscapulohumeral dystrophy: Activatin an early embryonictranscriptional program in human skeletal muscle” Human Mol Genet.(2018); and Tawil, R. “Facioscapulohumeral muscular dystrophy” HandbookClin. Neurol. (2018), 148: 541-548.) FSHD Type 1 is associated withOnline Mendelian Inheritance in Man (OMIM) Entry #158900. FSHD Type 2 isassociated with OMIM Entry #158901.

Framework: As used herein, the term “framework” or “framework sequence”refers to the remaining sequences of a variable region minus the CDRs.Because the exact definition of a CDR sequence can be determined bydifferent systems, the meaning of a framework sequence is subject tocorrespondingly different interpretations. The six CDRs (CDR-L1, CDR-L2,and CDR-L3 of light chain and CDR-H1, CDR-H2, and CDR-H3 of heavy chain)also divide the framework regions on the light chain and the heavy chaininto four sub-regions (FR1, 1-R2, FR3 and 1-R4) on each chain, in whichCDR1 is positioned between FR1 and FR2, CDR2 between FR2 and FR3, andCDR3 between FR3 and FR4. Without specifying the particular sub-regionsas FR1, 1-R2, FR3 or FR4, a framework region, as referred by others,represents the combined FRs within the variable region of a single,naturally occurring immunoglobulin chain. As used herein, a FRrepresents one of the four sub-regions, and FRs represents two or moreof the four sub-regions constituting a framework region. Human heavychain and light chain acceptor sequences are known in the art. In oneembodiment, the acceptor sequences known in the art may be used in theantibodies disclosed herein.

Human antibody: The term “human antibody”, as used herein, is intendedto include antibodies having variable and constant regions derived fromhuman germline immunoglobulin sequences. The human antibodies of thedisclosure may include amino acid residues not encoded by human germlineimmunoglobulin sequences (e.g., mutations introduced by random orsite-specific mutagenesis in vitro or by somatic mutation in vivo), forexample in the CDRs and in particular CDR3. However, the term “humanantibody”, as used herein, is not intended to include antibodies inwhich CDR sequences derived from the germline of another mammalianspecies, such as a mouse, have been grafted onto human frameworksequences.

Humanized antibody: The term “humanized antibody” refers to antibodieswhich comprise heavy and light chain variable region sequences from anon-human species (e.g., a mouse) but in which at least a portion of theVH and/or VL sequence has been altered to be more “human-like”, i.e.,more similar to human germline variable sequences. One type of humanizedantibody is a CDR-grafted antibody, in which human CDR sequences areintroduced into non-human VH and VL sequences to replace thecorresponding nonhuman CDR sequences. In one embodiment, humanizedanti-transferrin receptor antibodies and antigen binding portions areprovided. Such antibodies may be generated by obtaining murineanti-transferrin receptor monoclonal antibodies using traditionalhybridoma technology followed by humanization using in vitro geneticengineering, such as those disclosed in Kasaian et al PCT publicationNo. WO 2005/123126 A2.

Internalizing cell surface receptor: As used herein, the term,“internalizing cell surface receptor” refers to a cell surface receptorthat is internalized by cells, e.g., upon external stimulation, e.g.,ligand binding to the receptor. In some embodiments, an internalizingcell surface receptor is internalized by endocytosis. In someembodiments, an internalizing cell surface receptor is internalized byclathrin-mediated endocytosis. However, in some embodiments, aninternalizing cell surface receptor is internalized by aclathrin-independent pathway, such as, for example, phagocytosis,macropinocytosis, caveolae- and raft-mediated uptake or constitutiveclathrin-independent endocytosis. In some embodiments, the internalizingcell surface receptor comprises an intracellular domain, a transmembranedomain, and/or an extracellular domain, which may optionally furthercomprise a ligand-binding domain. In some embodiments, a cell surfacereceptor becomes internalized by a cell after ligand binding. In someembodiments, a ligand may be a muscle-targeting agent or amuscle-targeting antibody. In some embodiments, an internalizing cellsurface receptor is a transferrin receptor.

Isolated antibody: An “isolated antibody”, as used herein, is intendedto refer to an antibody that is substantially free of other antibodieshaving different antigenic specificities (e.g., an isolated antibodythat specifically binds transferrin receptor is substantially free ofantibodies that specifically bind antigens other than transferrinreceptor). An isolated antibody that specifically binds transferrinreceptor complex may, however, have cross-reactivity to other antigens,such as transferrin receptor molecules from other species. Moreover, anisolated antibody may be substantially free of other cellular materialand/or chemicals.

Kabat numbering: The terms “Kabat numbering”, “Kabat definitions and“Kabat labeling” are used interchangeably herein. These terms, which arerecognized in the art, refer to a system of numbering amino acidresidues which are more variable (i.e. hypervariable) than other aminoacid residues in the heavy and light chain variable regions of anantibody, or an antigen binding portion thereof (Kabat et al. (1971)Ann. NY Acad, Sci. 190:382-391 and, Kabat, E. A., et al. (1991)Sequences of Proteins of Immunological Interest, Fifth Edition, U.S.Department of Health and Human Services, NIH Publication No. 91-3242).For the heavy chain variable region, the hypervariable region rangesfrom amino acid positions 31 to 35 for CDR1, amino acid positions 50 to65 for CDR2, and amino acid positions 95 to 102 for CDR3. For the lightchain variable region, the hypervariable region ranges from amino acidpositions 24 to 34 for CDR1, amino acid positions 50 to 56 for CDR2, andamino acid positions 89 to 97 for CDR3.

Molecular payload: As used herein, the term “molecular payload” refersto a molecule or species that functions to modulate a biologicaloutcome. In some embodiments, a molecular payload is linked to, orotherwise associated with a muscle-targeting agent. In some embodiments,the molecular payload is a small molecule, a protein, a peptide, anucleic acid, or an oligonucleotide. In some embodiments, the molecularpayload functions to modulate the transcription of a DNA sequence, tomodulate the expression of a protein, or to modulate the activity of aprotein. In some embodiments, the molecular payload is anoligonucleotide that comprises a strand having a region ofcomplementarity to a target gene.

Muscle-targeting agent: As used herein, the term, “muscle-targetingagent,” refers to a molecule that specifically binds to an antigenexpressed on muscle cells. The antigen in or on muscle cells may be amembrane protein, for example an integral membrane protein or aperipheral membrane protein. Typically, a muscle-targeting agentspecifically binds to an antigen on muscle cells that facilitatesinternalization of the muscle-targeting agent (and any associatedmolecular payload) into the muscle cells. In some embodiments, amuscle-targeting agent specifically binds to an internalizing, cellsurface receptor on muscles and is capable of being internalized intomuscle cells through receptor mediated internalization. In someembodiments, the muscle-targeting agent is a small molecule, a protein,a peptide, a nucleic acid (e.g., an aptamer), or an antibody. In someembodiments, the muscle-targeting agent is linked to a molecularpayload.

Muscle-targeting antibody: As used herein, the term, “muscle-targetingantibody,” refers to a muscle-targeting agent that is an antibody thatspecifically binds to an antigen found in or on muscle cells. In someembodiments, a muscle-targeting antibody specifically binds to anantigen on muscle cells that facilitates internalization of themuscle-targeting antibody (and any associated molecular payment) intothe muscle cells. In some embodiments, the muscle-targeting antibodyspecifically binds to an internalizing, cell surface receptor present onmuscle cells. In some embodiments, the muscle-targeting antibody is anantibody that specifically binds to a transferrin receptor.

Oligonucleotide: As used herein, the term “oligonucleotide” refers to anoligomeric nucleic acid compound of up to 200 nucleotides in length.Examples of oligonucleotides include, but are not limited to, RNAioligonucleotides (e.g., siRNAs, shRNAs), microRNAs, gapmers, mixmers,phosphorodiamidite morpholinos, peptide nucleic acids, aptamers, guidenucleic acids (e.g., Cas9 guide RNAs), etc. Oligonucleotides may besingle-stranded or double-stranded. In some embodiments, anoligonucleotide may comprise one or more modified nucleotides (e.g.2′-O-methyl sugar modifications, purine or pyrimidine modifications). Insome embodiments, an oligonucleotide may comprise one or more modifiedinternucleotide linkage. In some embodiments, an oligonucleotide maycomprise one or more phosphorothioate linkages, which may be in the Rpor Sp stereochemical conformation.

Recombinant antibody: The term “recombinant human antibody”, as usedherein, is intended to include all human antibodies that are prepared,expressed, created or isolated by recombinant means, such as antibodiesexpressed using a recombinant expression vector transfected into a hostcell (described in more details in this disclosure), antibodies isolatedfrom a recombinant, combinatorial human antibody library (Hoogenboom H.R., (1997) TIB Tech. 15:62-70; Azzazy H., and Highsmith W. E., (2002)Clin. Biochem. 35:425-445; Gavilondo J. V., and Larrick J. W. (2002)BioTechniques 29:128-145; Hoogenboom H., and Chames P. (2000) ImmunologyToday 21:371-378), antibodies isolated from an animal (e.g., a mouse)that is transgenic for human immunoglobulin genes (see e.g., Taylor, L.D., et al. (1992) Nucl. Acids Res. 20:6287-6295; Kellermann S-A., andGreen L. L. (2002) Current Opinion in Biotechnology 13:593-597; LittleM. et al (2000) Immunology Today 21:364-370) or antibodies prepared,expressed, created or isolated by any other means that involves splicingof human immunoglobulin gene sequences to other DNA sequences. Suchrecombinant human antibodies have variable and constant regions derivedfrom human germline immunoglobulin sequences. In certain embodiments,however, such recombinant human antibodies are subjected to in vitromutagenesis (or, when an animal transgenic for human Ig sequences isused, in vivo somatic mutagenesis) and thus the amino acid sequences ofthe VH and VL regions of the recombinant antibodies are sequences that,while derived from and related to human germline VH and VL sequences,may not naturally exist within the human antibody germline repertoire invivo. One embodiment of the disclosure provides fully human antibodiescapable of binding human transferrin receptor which can be generatedusing techniques well known in the art, such as, but not limited to,using human Ig phage libraries such as those disclosed in Jermutus etal., PCT publication No. WO 2005/007699 A2.

Region of complementarity: As used herein, the term “region ofcomplementarity” refers to a nucleotide sequence, e.g., of aoligonucleotide, that is sufficiently complementary to a cognatenucleotide sequence, e.g., of a target nucleic acid, such that the twonucleotide sequences are capable of annealing to one another underphysiological conditions (e.g., in a cell). In some embodiments, aregion of complementarity is fully complementary to a cognate nucleotidesequence of target nucleic acid. However, in some embodiments, a regionof complementarity is partially complementary to a cognate nucleotidesequence of target nucleic acid (e.g., at least 80%, 90%, 95% or 99%complementarity). In some embodiments, a region of complementaritycontains 1, 2, 3, or 4 mismatches compared with a cognate nucleotidesequence of a target nucleic acid.

Specifically binds: As used herein, the term “specifically binds” refersto the ability of a molecule to bind to a binding partner with a degreeof affinity or avidity that enables the molecule to be used todistinguish the binding partner from an appropriate control in a bindingassay or other binding context. With respect to an antibody, the term,“specifically binds”, refers to the ability of the antibody to bind to aspecific antigen with a degree of affinity or avidity, compared with anappropriate reference antigen or antigens, that enables the antibody tobe used to distinguish the specific antigen from others, e.g., to anextent that permits preferential targeting to certain cells, e.g.,muscle cells, through binding to the antigen, as described herein. Insome embodiments, an antibody specifically binds to a target if theantibody has a K_(D) for binding the target of at least about 10⁻⁴ M,10⁻⁵ M, 10⁻⁶ M, 10⁻⁷ M, 10⁻⁸ M, 10⁻⁹ M, 10⁻¹⁰ M, 10⁻¹¹ M, 10⁻¹² M, 10⁻¹³M, or less. In some embodiments, an antibody specifically binds to thetransferrin receptor, e.g., an epitope of the apical domain oftransferrin receptor.

Subject: As used herein, the term “subject” refers to a mammal. In someembodiments, a subject is non-human primate, or rodent. In someembodiments, a subject is a human. In some embodiments, a subject is apatient, e.g., a human patient that has or is suspected of having adisease. In some embodiments, the subject is a human patient who has oris suspected of having FSHD.

Transferrin receptor: As used herein, the term, “transferrin receptor”(also known as TFRC, CD71, p90, or TFR1) refers to an internalizing cellsurface receptor that binds transferrin to facilitate iron uptake byendocytosis. In some embodiments, a transferrin receptor may be of human(NCBI Gene ID 7037), non-human primate (e.g., NCBI Gene ID 711568 orNCBI Gene ID 102136007), or rodent (e.g., NCBI Gene ID 22042) origin. Inaddition, multiple human transcript variants have been characterizedthat encoded different isoforms of the receptor (e.g., as annotatedunder GenBank RefSeq Accession Numbers: NP_001121620.1, NP_003225.2,NP_001300894.1, and NP_001300895.1).

II. Complexes

Provided herein are complexes that comprise a targeting agent, e.g. anantibody, covalently linked to a molecular payload. In some embodiments,a complex comprises a muscle-targeting antibody covalently linked to aoligonucleotide. A complex may comprise an antibody that specificallybinds a single antigenic site or that binds to at least two antigenicsites that may exist on the same or different antigens.

A complex may be used to modulate the activity or function of at leastone gene, protein, and/or nucleic acid. In some embodiments, themolecular payload present with a complex is responsible for themodulation of a gene, protein, and/or nucleic acids. A molecular payloadmay be a small molecule, protein, nucleic acid, oligonucleotide, or anymolecular entity capable of modulating the activity or function of agene, protein, and/or nucleic acid in a cell. In some embodiments, amolecular payload is an oligonucleotide that targets a DUX4 in musclecells.

In some embodiments, a complex comprises a muscle-targeting agent, e.g.an anti-transferrin receptor antibody, covalently linked to a molecularpayload, e.g. an antisense oligonucleotide that targets a DUX4.

A. Muscle-Targeting Agents

Some aspects of the disclosure provide muscle-targeting agents, e.g.,for delivering a molecular payload to a muscle cell. In someembodiments, such muscle-targeting agents are capable of binding to amuscle cell, e.g., via specifically binding to an antigen on the musclecell, and delivering an associated molecular payload to the muscle cell.In some embodiments, the molecular payload is bound (e.g., covalentlybound) to the muscle targeting agent and is internalized into the musclecell upon binding of the muscle targeting agent to an antigen on themuscle cell, e.g., via endocytosis. It should be appreciated thatvarious types of muscle-targeting agents may be used in accordance withthe disclosure. For example, the muscle-targeting agent may comprise, orconsist of, a nucleic acid (e.g., DNA or RNA), a peptide (e.g., anantibody), a lipid (e.g., a microvesicle), or a sugar moiety (e.g., apolysaccharide). Exemplary muscle-targeting agents are described infurther detail herein, however, it should be appreciated that theexemplary muscle-targeting agents provided herein are not meant to belimiting.

Some aspects of the disclosure provide muscle-targeting agents thatspecifically bind to an antigen on muscle, such as skeletal muscle,smooth muscle, or cardiac muscle. In some embodiments, any of themuscle-targeting agents provided herein bind to (e.g., specifically bindto) an antigen on a skeletal muscle cell, a smooth muscle cell, and/or acardiac muscle cell.

By interacting with muscle-specific cell surface recognition elements(e.g., cell membrane proteins), both tissue localization and selectiveuptake into muscle cells can be achieved. In some embodiments, moleculesthat are substrates for muscle uptake transporters are useful fordelivering a molecular payload into muscle tissue. Binding to musclesurface recognition elements followed by endocytosis can allow evenlarge molecules such as antibodies to enter muscle cells. As anotherexample molecular payloads conjugated to transferrin or anti-transferrinreceptor antibodies can be taken up by muscle cells via binding totransferrin receptor, which may then be endocytosed, e.g., viaclathrin-mediated endocytosis.

The use of muscle-targeting agents may be useful for concentrating amolecular payload (e.g., oligonucleotide) in muscle while reducingtoxicity associated with effects in other tissues. In some embodiments,the muscle-targeting agent concentrates a bound molecular payload inmuscle cells as compared to another cell type within a subject. In someembodiments, the muscle-targeting agent concentrates a bound molecularpayload in muscle cells (e.g., skeletal, smooth, or cardiac musclecells) in an amount that is at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15,20, 30, 40, 50, 60, 70, 80, 90, or 100 times greater than an amount innon-muscle cells (e.g., liver, neuronal, blood, or fat cells). In someembodiments, a toxicity of the molecular payload in a subject is reducedby at least 1%, 2%, 3%, 4%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%,50%, 55%, 60%, 65%, 70%, 75%, 80%, 90%, or 95% when it is delivered tothe subject when bound to the muscle-targeting agent.

In some embodiments, to achieve muscle selectivity, a muscle recognitionelement (e.g., a muscle cell antigen) may be required. As one example, amuscle-targeting agent may be a small molecule that is a substrate for amuscle-specific uptake transporter. As another example, amuscle-targeting agent may be an antibody that enters a muscle cell viatransporter-mediated endocytosis. As another example, a muscle targetingagent may be a ligand that binds to cell surface receptor on a musclecell. It should be appreciated that while transporter-based approachesprovide a direct path for cellular entry, receptor-based targeting mayinvolve stimulated endocytosis to reach the desired site of action.

i. Muscle-Targeting Antibodies

In some embodiments, the muscle-targeting agent is an antibody.Generally, the high specificity of antibodies for their target antigenprovides the potential for selectively targeting muscle cells (e.g.,skeletal, smooth, and/or cardiac muscle cells). This specificity mayalso limit off-target toxicity. Examples of antibodies that are capableof targeting a surface antigen of muscle cells have been reported andare within the scope of the disclosure. For example, antibodies thattarget the surface of muscle cells are described in Arahata K., et al.“Immunostaining of skeletal and cardiac muscle surface membrane withantibody against Duchenne muscular dystrophy peptide” Nature 1988; 333:861-3; Song K. S., et al. “Expression of caveolin-3 in skeletal,cardiac, and smooth muscle cells. Caveolin-3 is a component of thesarcolemma and co-fractionates with dystrophin and dystrophin-associatedglycoproteins” J Biol Chem 1996; 271: 15160-5; and Weisbart R. H. etal., “Cell type specific targeted intracellular delivery into muscle ofa monoclonal antibody that binds myosin IIb” Mol Immunol. 2003 March,39(13):78309; the entire contents of each of which are incorporatedherein by reference.

a. Anti-Transferrin Receptor Antibodies

Some aspects of the disclosure are based on the recognition that agentsbinding to transferrin receptor, e.g., anti-transferrin-receptorantibodies, are capable of targeting muscle cell. Transferrin receptorsare internalizing cell surface receptors that transport transferrinacross the cellular membrane and participate in the regulation andhomeostasis of intracellular iron levels. Some aspects of the disclosureprovide transferrin receptor binding proteins, which are capable ofbinding to transferrin receptor. Accordingly, aspects of the disclosureprovide binding proteins (e.g., antibodies) that bind to transferrinreceptor. In some embodiments, binding proteins that bind to transferrinreceptor are internalized, along with any bound molecular payload, intoa muscle cell. As used herein, an antibody that binds to a transferrinreceptor may be referred to as an anti-transferrin receptor antibody.Antibodies that bind, e.g. specifically bind, to a transferrin receptormay be internalized into the cell, e.g. through receptor-mediatedendocytosis, upon binding to a transferrin receptor.

It should be appreciated that anti-transferrin receptor antibodies maybe produced, synthesized, and/or derivatized using several knownmethodologies, e.g. library design using phage display. Exemplarymethodologies have been characterized in the art and are incorporated byreference (Díez, P. et al. “High-throughput phage-display screening inarray format”, Enzyme and microbial technology, 2015, 79, 34-41.;Christoph M. H. and Stanley, J. R. “Antibody Phage Display: Techniqueand Applications” J Invest Dermatol. 2014, 134:2.; Engleman, Edgar (Ed.)“Human Hybridomas and Monoclonal Antibodies.” 1985, Springer.). In otherembodiments, an anti-transferrin antibody has been previouslycharacterized or disclosed. Antibodies that specifically bind totransferrin receptor are known in the art (see, e.g. U.S. Pat. No.4,364,934, filed Dec. 4, 1979, “Monoclonal antibody to a human earlythymocyte antigen and methods for preparing same”; U.S. Pat. No.8,409,573, filed Jun. 14, 2006, “Anti-CD71 monoclonal antibodies anduses thereof for treating malignant tumor cells”; U.S. Pat. No.9,708,406, filed May 20, 2014, “Anti-transferrin receptor antibodies andmethods of use”; U.S. Pat. No. 9,611,323, filed Dec. 19, 2014, “Lowaffinity blood brain barrier receptor antibodies and uses therefor”; WO2015/098989, filed Dec. 24, 2014, “Novel anti-Transferrin receptorantibody that passes through blood-brain barrier”; Schneider C. et al.“Structural features of the cell surface receptor for transferrin thatis recognized by the monoclonal antibody OKT9.” J Biol Chem. 1982,257:14, 8516-8522.; Lee et al. “Targeting Rat Anti-Mouse TransferrinReceptor Monoclonal Antibodies through Blood-Brain Barrier in Mouse”2000, J Pharmacol. Exp. Ther., 292: 1048-1052.).

Any appropriate anti-transferrin receptor antibodies may be used in thecomplexes disclosed herein. Examples of anti-transferrin receptorantibodies, including associated references and binding epitopes, arelisted in Table 1. In some embodiments, the anti-transferrin receptorantibody comprises the complementarity determining regions (CDR-H1,CDR-H2, CDR-H3, CDR-L1, CDR-L2, and CDR-L3) of any of theanti-transferrin receptor antibodies provided herein, e.g.,anti-transferrin receptor antibodies listed in Table 1.

TABLE 1 List of anti-transferrin receptor antibody clones, includingassociated references and binding epitope information. Antibody CloneName Reference(s) Epitope/Notes OKT9 U.S. Pat. No. 4,364,934, filed Dec.4, 1979, Apical domain of TfR entitled “MONOCLONAL ANTIBODY (residues305-366 of TO A HUMAN EARLY THYMOCYTE human TfR sequence ANTIGEN ANDMETHODS FOR XM_052730.3, PREPARING SAME” available in GenBank) SchneiderC. et al. “Structural features of the cell surface receptor fortransferrin that is recognized by the monoclonal antibody OKT9.” J BiolChem. 1982, 257:14, 8516-8522. (From JCR) WO 2015/098989, filed Apicaldomain Clone M11 Dec. 24, 2014, “Novel anti-Transferrin (residues230-244 and Clone M23 receptor antibody that passes through 326-347 ofTfR) and Clone M27 blood-brain barrier” protease-like domain Clone B84U.S. Pat. No. 9,994,641, filed (residues 461-473) Dec. 24, 2014, “Novelanti-Transferrin receptor antibody that passes through blood-brainbarrier” (From WO 016/081643, filed May 26, 2016, 2 Apical domain andGenentech) entitled “ANTI-TRANSFERRIN non-apical regions Clones 7A4,RECEPTOR ANTIBODIES AND 8A2, 15D2, METHODS OF USE” 10D11, 7B10, U.S.Pat. No. 9,708,406, filed 15G11, 16G5, May 20, 2014, “Anti-transferrinreceptor 13C3, 16G4, antibodies and methods of use” 16F6, 7G7, 4C2,1B12, and 13D4 (From Lee et al. “Targeting Rat Anti- Armagen) MouseTransferrin Receptor Monoclonal 8D3 Antibodies through Blood-BrainBarrier in Mouse” 2000, J Pharmacol. Exp. Ther., 292: 1048-1052. U.S.patent application 2010/077498, filed Sep. 11, 2008, entitled“COMPOSITIONS AND METHODS FOR BLOOD-BRAIN BARRIER DELIVERY IN THE MOUSE”OX26 Haobam, B. et al. 2014. Rab17- mediated recycling endosomescontribute to autophagosome formation in response to Group AStreptococcus invasion. Cellular microbiology. 16: 1806-21. DF1513Ortiz-Zapater E et al. Trafficking of the human transferrin receptor inplant cells: effects of tyrphostin A23 and brefeldin A. Plant J48:757-70 (2006). 1A1B2, Commercially available anti- Novus Biologicals66IG10, transferrin receptor antibodies. 8100 Southpark Way, MEM-189,A-8 Littleton CO JF0956, 29806, 80120 1A1B2, TFRC/1818, 1E6, 66Ig10,TFRC/1059, Q1/71, 23D10, 13E4, TFRC/1149, ER-MP21, YTA74.4, BU54, 2B6,RI7 217 (From U.S. patent application 2011/0311544A1, Does not competeINSERM) filed Jun. 15, 2005, entitled “ANTI-CD71 with OKT9 BA120gMONOCLONAL ANTIBODIES AND USES THEREOF FOR TREATING MALIGNANT TUMORCELLS” LUCA31 U.S. Pat. No. 7,572,895, filed “LUCA31 epitope” Jun. 7,2004, entitled “TRANSFERRIN RECEPTOR ANTIBODIES” (Salk Institute)Trowbridge, I.S. et al. “Anti-transferrin B3/25 receptor monoclonalantibody and T58/30 toxin-antibody conjugates affect growth of humantumour cells.” Nature, 1981, volume 294, pages 171-173 R17 217.1.3,Commercially available anti- BioXcell 5E9C11, transferrin receptorantibodies. 10 Technology Dr., OKT9 Suite 2B (BE0023 West Lebanon, NHclone) 03784-1671 USA BK19.9, Gatter, K.C. et al. “Transferrin B3/25,T56/14 receptors in human tissues: their and T58/1 distribution andpossible clinical relevance.” J Clin Pathol. 1983 May; 36(5):539-45.

In some embodiments, the muscle-targeting agent is an anti-transferrinreceptor antibody. In some embodiment, an anti-transferrin receptorantibody specifically binds to a transferrin protein having an aminoacid sequence as disclosed herein. In some embodiments, ananti-transferrin receptor antibody may specifically bind to anyextracellular epitope of a transferrin receptor or an epitope thatbecomes exposed to an antibody, including the apical domain, thetransferrin binding domain, and the protease-like domain. In someembodiments, an anti-transferrin receptor antibody binds to an aminoacid segment of a human or non-human primate transferrin receptor, asprovided in SEQ ID Nos. 1-3 in the range of amino acids C89 to F760. Insome embodiments, an anti-transferrin receptor antibody specificallybinds with binding affinity of at least about 10⁻⁴ M, 10⁻⁵ M, 10⁻⁶ M,10⁻⁷ M, 10⁻⁸ M, 10⁻⁹ M, 10⁻¹⁰ M, 10⁻¹¹ M, 10⁻¹² M, 10⁻¹³ M, or less.Anti-transferrin receptor antibodies used herein may be capable ofcompeting for binding with other anti-transferrin receptor antibodies,e.g. OKT9, 8D3, that bind to transferrin receptor with 10⁻³ M, 10⁻⁴ M,10⁻⁵ M, 10⁻⁶ M, 10⁻⁷ M, or less.

An example human transferrin receptor amino acid sequence, correspondingto NCBI sequence NP_003225.2 (transferrin receptor protein 1 isoform 1,Homo sapiens) is as follows:

(SEQ ID NO: 1) MMDQARSAFSNLFGGEPLSYTRFSLARQVDGDNSHVEMKLAVDEEENADNNTKANVTKPKRCSGSICYGTIAVIVFFLIGFMIGYLGYCKGVEPKTECERLAGTESPVREEPGEDFPAARRLYWDDLKRKLSEKLDSTDFTGTIKLLNENSYVPREAGSQKDENLALYVENQFREFKLSKVWRDQHFVKIQVKDSAQNSVIIVDKNGRLVYLVENPGGYVAYSKAATVTGKLVHANFGTKKDFEDLYTPVNGSIVIVRAGKITFAEKVANAESLNAIGVLIYMDQTKFPIVNAELSFFGHAHLGTGDPYTPGFPSFNHTQFPPSRSSGLPNIPVQTISRAAAEKLFGNMEGDCPSDWKTDSTCRMVTSESKNVKLTVSNVLKEIKILNIFGVIKGFVEPDHYVVVGAQRDAWGPGAAKSGVGTALLLKLAQMFSDMVLKDGFQPSRSIIFASWSAGDFGSVGATEWLEGYLSSLHLKAFTYINLDKAVLGTSNFKVSASPLLYTLIEKTMQNVKHPVTGQFLYQDSNWASKVEKLTLDNAAFPFLAYSGIPAVSFCFCEDTDYPYLGTTMDTYKELIERIPELNKVARAAAEVAGQFVIKLTHDVELNLDYERYNSQLLSFVRDLNQYRADIKEMGLSLQWLYSARGDFFRATSRLTTDFGNAEKTDRFVMKKLNDRVMRVEYHFLSPYVSPKESPFRHVFWGSGSHTLPALLENLKLRKQNNGAFNETLFRNQLALATWTIQGAANALSGDVWDIDNEF

An example non-human primate transferrin receptor amino acid sequence,corresponding to NCBI sequence NP_001244232.1 (transferrin receptorprotein 1, Macaca mulatta) is as follows:

(SEQ ID NO: 2) MMDQARSAFSNLFGGEPLSYTRFSLARQVDGDNSHVEMKLGVDEEENTDNNTKPNGTKPKRCGGNICYGTIAVIIFFLIGFMIGYLGYCKGVEPKTECERLAGTESPAREEPEEDFPAAPRLYWDDLKRKLSEKLDTTDFTSTIKLLNENLYVPREAGSQKDENLALYIENQFREFKLSKVWRDQHFVKIQVKDSAQNSVIIVDKNGGLVYLVENPGGYVAYSKAATVTGKLVHANFGTKKDFEDLDSPVNGSIVIVRAGKITFAEKVANAESLNAIGVLIYMDQTKFPIVKADLSFFGHAHLGTGDPYTPGFPSFNHTQFPPSQSSGLPNIPVQTISRAAAEKLFGNMEGDCPSDWKTDSTCKMVTSENKSVKLTVSNVLKETKILNIFGVIKGFVEPDHYVVVGAQRDAWGPGAAKSSVGTALLLKLAQMFSDMVLKDGFQPSRSIIFASWSAGDFGSVGATEWLEGYLSSLHLKAFTYINLDKAVLGTSNFKVSASPLLYTLIEKTMQDVKHPVTGRSLYQDSNWASKVEKLTLDNAAFPFLAYSGIPAVSFCFCEDTDYPYLGTTMDTYKELVERIPELNKVARAAAEVAGQFVIKLTHDTELNLDYERYNSQLLLFLRDLNQYRADVKEMGLSLQWLYSARGDFFRATSRLTTDFRNAEKRDKFVMKKLNDRVMRVEYYFLSPYVSPKESPFRHVFWGSGSHTLSALLESLKLRRQNNSAFNETLFRNQLALATWTIQGAANALSGDVWDIDNEF

An example non-human primate transferrin receptor amino acid sequence,corresponding to NCBI sequence XP_005545315.1 (transferrin receptorprotein 1, Macaca fascicularis) is as follows:

(SEQ ID NO: 3) MMDQARSAFSNLFGGEPLSYTRFSLARQVDGDNSHVEMKLGVDEEENTDNNTKANGTKPKRCGGNICYGTIAVIIFFLIGFMIGYLGYCKGVEPKTECERLAGTESPAREEPEEDFPAAPRLYWDDLKRKLSEKLDTTDFTSTIKLLNENLYVPREAGSQKDENLALYIENQFREFKLSKVWRDQHFVKIQVKDSAQNSVIIVDKNGGLVYLVENPGGYVAYSKAATVTGKLVHANFGTKKDFEDLDSPVNGSIVIVRAGKITFAEKVANAESLNAIGVLIYMDQTKFPIVKADLSFFGHAHLGTGDPYTPGFPSFNHTQFPPSQSSGLPNIPVQTISRAAAEKLFGNMEGDCPSDWKTDSTCKMVTSENKSVKLTVSNVLKETKILNIFGVIKGFVEPDHYVVVGAQRDAWGPGAAKSSVGTALLLKLAQMFSDMVLKDGFQPSRSIIFASWSAGDFGSVGATEWLEGYLSSLHLKAFTYINLDKAVLGTSNFKVSASPLLYTLIEKTMQDVKHPVTGRSLYQDSNWASKVEKLTLDNAAFPFLAYSWAYSFCFCEDTDYPYLGTTMDTYKELVERIPELNKVARAAAEVAGQFVIKLTHDTELNLDYERYNSQLLLFLRDLNQYRADVKEMGLSLQWLYSARGDFFRATSRLTTDFRNAEKRDKFVMKKLNDRVMRVEYYFLSPYVSPKESPFRHVFWGSGSHTLSALLESLKLRRQNNSAFNETLFRNQLALATWTIQGAANALSGDVWDIDNEF.

An example mouse transferrin receptor amino acid sequence, correspondingto NCBI sequence NP_001344227.1 (transferrin receptor protein 1, Musmusculus) is as follows:

(SEQ ID NO: 4) MMDQARSAFSNLFGGEPLSYTRFSLARQVDGDNSHVEMKLAADEEENADNNMKASVRKPKRFNGRLCFAAIALVIFFLIGFMSGYLGYCKRVEQKEECVKLAETEETDKSETMETEDVPTSSRLYWADLKTLLSEKLNSIEFADTIKQLSQNTYTPREAGSQKDESLAYYIENQFHEFKFSKVWRDEHYVKIQVKSSIGQNMVTIVQSNGNLDPVESPEGYVAFSKPTEVSGKLVHANFGTKKDFEELSYSVNGSLVIVRAGEITFAEKVANAQSFNAIGVLIYMDKNKFPVVEADLALFGHAHLGTGDPYTPGFPSFNHTQFPPSQSSGLPNIPVQTISRAAAEKLFGKMEGSCPARWNIDSSCKLELSQNQNVKLIVKNVLKERRILNIFGVIKGYEEPDRYVVVGAQRDALGAGVAAKSSVGTGLLLKLAQVFSDMISKDGFRPSRSIIFASWTAGDFGAVGATEWLEGYLSSLHLKAFTYINLDKVVLGTSNFKVSASPLLYTLMGKIMQDVKHPVDGKSLYRDSNWISKVEKLSFDNAAYPFLAYSGIPAVSFCFCEDADYPYLGTRLDTYEALTQKVPQLNQMVRTAAEVAGQLIIKLTHDVELNLDYEMYNSKLLSFMKDLNQFKTDIRDMGLSLQWLYSARGDYFRATSRLTTDFHNAEKTNRFVMREINDRIMKVEYHFLSPYVSPRESPFRHIFWGSGSHTLSALVENLKLRQKNITAFNETLFRNQLALATWTIQGVANALSGDIWNIDNEF

In some embodiments, an anti-transferrin receptor antibody binds to anamino acid segment of the receptor as follows:FVKIQVKDSAQNSVIIVDKNGRLVYLVENPGGYVAYSKAATVTGKLVHANFGTKKDFEDLYTPVNGSIVIVRAGKITFAEKVANAESLNAIGVLIYMDQTKFPIVNAELSFFGHAHLGTGDPYTPGFPSFNHTQFPPSRSSGLPNIPVQTISRAAAEKLFGNMEGDCPSDWKTDSTCRMVTSESKNVKLTVSNVLKE (SEQ ID NO: 5) and does not inhibit the bindinginteractions between transferrin receptors and transferrin and/or humanhemochromatosis protein (also known as HFE).

Appropriate methodologies may be used to obtain and/or produceantibodies, antibody fragments, or antigen-binding agents, e.g., throughthe use of recombinant DNA protocols. In some embodiments, an antibodymay also be produced through the generation of hybridomas (see, e.g.,Kohler, G and Milstein, C. “Continuous cultures of fused cells secretingantibody of predefined specificity” Nature, 1975, 256: 495-497). Theantigen-of-interest may be used as the immunogen in any form or entity,e.g., recombinant or a naturally occurring form or entity. Hybridomasare screened using standard methods, e.g. ELISA screening, to find atleast one hybridoma that produces an antibody that targets a particularantigen. Antibodies may also be produced through screening of proteinexpression libraries that express antibodies, e.g., phage displaylibraries. Phage display library design may also be used, in someembodiments, (see, e.g. U.S. Pat. No. 5,223,409, filed Mar. 1, 1991,“Directed evolution of novel binding proteins”; WO 1992/18619, filedApr. 10, 1992, “Heterodimeric receptor libraries using phagemids”; WO1991/17271, filed May 1, 1991, “Recombinant library screening methods”;WO 1992/20791, filed May 15, 1992, “Methods for producing members ofspecific binding pairs”; WO 1992/15679, filed Feb. 28, 1992, and“Improved epitope displaying phage”). In some embodiments, anantigen-of-interest may be used to immunize a non-human animal, e.g., arodent or a goat. In some embodiments, an antibody is then obtained fromthe non-human animal, and may be optionally modified using a number ofmethodologies, e.g., using recombinant DNA techniques. Additionalexamples of antibody production and methodologies are known in the art(see, e.g. Harlow et al. “Antibodies: A Laboratory Manual”, Cold SpringHarbor Laboratory, 1988.).

In some embodiments, an antibody is modified, e.g., modified viaglycosylation, phosphorylation, sumoylation, and/or methylation. In someembodiments, an antibody is a glycosylated antibody, which is conjugatedto one or more sugar or carbohydrate molecules. In some embodiments, theone or more sugar or carbohydrate molecule are conjugated to theantibody via N-glycosylation, O-glycosylation, C-glycosylation,glypiation (GPI anchor attachment), and/or phosphoglycosylation. In someembodiments, the one or more sugar or carbohydrate molecules aremonosaccharides, disaccharides, oligosaccharides, or glycans. In someembodiments, the one or more sugar or carbohydrate molecule is abranched oligosaccharide or a branched glycan. In some embodiments, theone or more sugar or carbohydrate molecule includes a mannose unit, aglucose unit, an N-acetylglucosamine unit, an N-acetylgalactosamineunit, a galactose unit, a fucose unit, or a phospholipid unit. In someembodiments, there are about 1-10, about 1-5, about 5-10, about 1-4,about 1-3, or about 2 sugar molecules. In some embodiments, aglycosylated antibody is fully or partially glycosylated. In someembodiments, an antibody is glycosylated by chemical reactions or byenzymatic means. In some embodiments, an antibody is glycosylated invitro or inside a cell, which may optionally be deficient in an enzymein the N- or O-glycosylation pathway, e.g. a glycosyltransferase. Insome embodiments, an antibody is functionalized with sugar orcarbohydrate molecules as described in International Patent ApplicationPublication WO2014065661, published on May 1, 2014, entitled, “Modifiedantibody, antibody-conjugate and process for the preparation thereof”.

Some aspects of the disclosure provide proteins that bind to transferrinreceptor (e.g., an extracellular portion of the transferrin receptor).In some embodiments, transferrin receptor antibodies provided hereinbind specifically to transferrin receptor (e.g., human transferrinreceptor). Transferrin receptors are internalizing cell surfacereceptors that transport transferrin across the cellular membrane andparticipate in the regulation and homeostasis of intracellular ironlevels. In some embodiments, transferrin receptor antibodies providedherein bind specifically to transferrin receptor from human, non-humanprimates, mouse, rat, etc. In some embodiments, transferrin receptorantibodies provided herein bind to human transferrin receptor. In someembodiments, transferrin receptor antibodies provided hereinspecifically bind to human transferrin receptor. In some embodiments,transferrin receptor antibodies provided herein bind to an apical domainof human transferrin receptor. In some embodiments, transferrin receptorantibodies provided herein specifically bind to an apical domain ofhuman transferrin receptor.

In some embodiments, transferrin receptor antibodies of the presentdisclosure include one or more of the CDR-H (e.g., CDR-H1, CDR-H2, andCDR-H3) amino acid sequences from any one of the anti-transferrinreceptor antibodies selected from Table 1. In some embodiments,transferrin receptor antibodies include the CDR-H1, CDR-H2, and CDR-H3as provided for any one of the anti-transferrin receptor antibodiesselected from Table 1. In some embodiments, anti-transferrin receptorantibodies include the CDR-L1, CDR-L2, and CDR-L3 as provided for anyone of the anti-transferrin receptor antibodies selected from Table 1.In some embodiments, anti-transferrin antibodies include the CDR-H1,CDR-H2, CDR-H3, CDR-L1, CDR-L2, and CDR-L3 as provided for any one ofthe anti-transferrin receptor antibodies selected from Table 1. Thedisclosure also includes any nucleic acid sequence that encodes amolecule comprising a CDR-H1, CDR-H2, CDR-H3, CDR-L1, CDR-L2, or CDR-L3as provided for any one of the anti-transferrin receptor antibodiesselected from Table 1. In some embodiments, antibody heavy and lightchain CDR3 domains may play a particularly important role in the bindingspecificity/affinity of an antibody for an antigen. Accordingly,anti-transferrin receptor antibodies of the disclosure may include atleast the heavy and/or light chain CDR3s of any one of theanti-transferrin receptor antibodies selected from Table 1.

In some examples, any of the anti-transferrin receptor antibodies of thedisclosure have one or more CDR (e.g., CDR-H or CDR-L) sequencessubstantially similar to any of the CDR-H1, CDR-H2, CDR-H3, CDR-L1,CDR-L2, and/or CDR-L3 sequences from one of the anti-transferrinreceptor antibodies selected from Table 1. In some embodiments, theposition of one or more CDRs along the VH (e.g., CDR-H1, CDR-H2, orCDR-H3) and/or VL (e.g., CDR-L1, CDR-L2, or CDR-L3) region of anantibody described herein can vary by one, two, three, four, five, orsix amino acid positions so long as immunospecific binding totransferrin receptor (e.g., human transferrin receptor) is maintained(e.g., substantially maintained, for example, at least 50%, at least60%, at least 70%, at least 80%, at least 90%, at least 95% of thebinding of the original antibody from which it is derived). For example,in some embodiments, the position defining a CDR of any antibodydescribed herein can vary by shifting the N-terminal and/or C-terminalboundary of the CDR by one, two, three, four, five, or six amino acids,relative to the CDR position of any one of the antibodies describedherein, so long as immunospecific binding to transferrin receptor (e.g.,human transferrin receptor) is maintained (e.g., substantiallymaintained, for example, at least 50%, at least 60%, at least 70%, atleast 80%, at least 90%, at least 95% of the binding of the originalantibody from which it is derived). In another embodiment, the length ofone or more CDRs along the VH (e.g., CDR-H1, CDR-H2, or CDR-H3) and/orVL (e.g., CDR-L1, CDR-L2, or CDR-L3) region of an antibody describedherein can vary (e.g., be shorter or longer) by one, two, three, four,five, or more amino acids, so long as immunospecific binding totransferrin receptor (e.g., human transferrin receptor) is maintained(e.g., substantially maintained, for example, at least 50%, at least60%, at least 70%, at least 80%, at least 90%, at least 95% of thebinding of the original antibody from which it is derived).

Accordingly, in some embodiments, a CDR-L1, CDR-L2, CDR-L3, CDR-H1,CDR-H2, and/or CDR-H3 described herein may be one, two, three, four,five or more amino acids shorter than one or more of the CDRs describedherein (e.g., CDRS from any of the anti-transferrin receptor antibodiesselected from Table 1) so long as immunospecific binding to transferrinreceptor (e.g., human transferrin receptor) is maintained (e.g.,substantially maintained, for example, at least 50%, at least 60%, atleast 70%, at least 80%, at least 90%, at least 95% relative to thebinding of the original antibody from which it is derived). In someembodiments, a CDR-L1, CDR-L2, CDR-L3, CDR-H1, CDR-H2, and/or CDR-H3described herein may be one, two, three, four, five or more amino acidslonger than one or more of the CDRs described herein (e.g., CDRS fromany of the anti-transferrin receptor antibodies selected from Table 1)so long as immunospecific binding to transferrin receptor (e.g., humantransferrin receptor) is maintained (e.g., substantially maintained, forexample, at least 50%, at least 60%, at least 70%, at least 80%, atleast 90%, at least 95% relative to the binding of the original antibodyfrom which it is derived). In some embodiments, the amino portion of aCDR-L1, CDR-L2, CDR-L3, CDR-H1, CDR-H2, and/or CDR-H3 described hereincan be extended by one, two, three, four, five or more amino acidscompared to one or more of the CDRs described herein (e.g., CDRS fromany of the anti-transferrin receptor antibodies selected from Table 1)so long as immunospecific binding to transferrin receptor (e.g., humantransferrin receptor is maintained (e.g., substantially maintained, forexample, at least 50%, at least 60%, at least 70%, at least 80%, atleast 90%, at least 95% relative to the binding of the original antibodyfrom which it is derived). In some embodiments, the carboxy portion of aCDR-L1, CDR-L2, CDR-L3, CDR-H1, CDR-H2, and/or CDR-H3 described hereincan be extended by one, two, three, four, five or more amino acidscompared to one or more of the CDRs described herein (e.g., CDRS fromany of the anti-transferrin receptor antibodies selected from Table 1)so long as immunospecific binding to transferrin receptor (e.g., humantransferrin receptor) is maintained (e.g., substantially maintained, forexample, at least 50%, at least 60%, at least 70%, at least 80%, atleast 90%, at least 95% relative to the binding of the original antibodyfrom which it is derived). In some embodiments, the amino portion of aCDR-L1, CDR-L2, CDR-L3, CDR-H1, CDR-H2, and/or CDR-H3 described hereincan be shortened by one, two, three, four, five or more amino acidscompared to one or more of the CDRs described herein (e.g., CDRS fromany of the anti-transferrin receptor antibodies selected from Table 1)so long as immunospecific binding to transferrin receptor (e.g., humantransferrin receptor) is maintained (e.g., substantially maintained, forexample, at least 50%, at least 60%, at least 70%, at least 80%, atleast 90%, at least 95% relative to the binding of the original antibodyfrom which it is derived). In some embodiments, the carboxy portion of aCDR-L1, CDR-L2, CDR-L3, CDR-H1, CDR-H2, and/or CDR-H3 described hereincan be shortened by one, two, three, four, five or more amino acidscompared to one or more of the CDRs described herein (e.g., CDRS fromany of the anti-transferrin receptor antibodies selected from Table 1)so long as immunospecific binding to transferrin receptor (e.g., humantransferrin receptor) is maintained (e.g., substantially maintained, forexample, at least 50%, at least 60%, at least 70%, at least 80%, atleast 90%, at least 95% relative to the binding of the original antibodyfrom which it is derived). Any method can be used to ascertain whetherimmunospecific binding to transferrin receptor (e.g., human transferrinreceptor) is maintained, for example, using binding assays andconditions described in the art.

In some examples, any of the anti-transferrin receptor antibodies of thedisclosure have one or more CDR (e.g., CDR-H or CDR-L) sequencessubstantially similar to any one of the anti-transferrin receptorantibodies selected from Table 1. For example, the antibodies mayinclude one or more CDR sequence(s) from any of the anti-transferrinreceptor antibodies selected from Table 1 containing up to 5, 4, 3, 2,or 1 amino acid residue variations as compared to the corresponding CDRregion in any one of the CDRs provided herein (e.g., CDRs from any ofthe anti-transferrin receptor antibodies selected from Table 1) so longas immunospecific binding to transferrin receptor (e.g., humantransferrin receptor) is maintained (e.g., substantially maintained, forexample, at least 50%, at least 60%, at least 70%, at least 80%, atleast 90%, at least 95% relative to the binding of the original antibodyfrom which it is derived). In some embodiments, any of the amino acidvariations in any of the CDRs provided herein may be conservativevariations. Conservative variations can be introduced into the CDRs atpositions where the residues are not likely to be involved ininteracting with a transferrin receptor protein (e.g., a humantransferrin receptor protein), for example, as determined based on acrystal structure. Some aspects of the disclosure provide transferrinreceptor antibodies that comprise one or more of the heavy chainvariable (VH) and/or light chain variable (VL) domains provided herein.In some embodiments, any of the VH domains provided herein include oneor more of the CDR-H sequences (e.g., CDR-H1, CDR-H2, and CDR-H3)provided herein, for example, any of the CDR-H sequences provided in anyone of the anti-transferrin receptor antibodies selected from Table 1.In some embodiments, any of the VL domains provided herein include oneor more of the CDR-L sequences (e.g., CDR-L1, CDR-L2, and CDR-L3)provided herein, for example, any of the CDR-L sequences provided in anyone of the anti-transferrin receptor antibodies selected from Table 1.

In some embodiments, anti-transferrin receptor antibodies of thedisclosure include any antibody that includes a heavy chain variabledomain and/or a light chain variable domain of any anti-transferrinreceptor antibody, such as any one of the anti-transferrin receptorantibodies selected from Table 1. In some embodiments, anti-transferrinreceptor antibodies of the disclosure include any antibody that includesthe heavy chain variable and light chain variable pairs of anyanti-transferrin receptor antibody, such as any one of theanti-transferrin receptor antibodies selected from Table 1.

Aspects of the disclosure provide anti-transferrin receptor antibodieshaving a heavy chain variable (VH) and/or a light chain variable (VL)domain amino acid sequence homologous to any of those described herein.In some embodiments, the anti-transferrin receptor antibody comprises aheavy chain variable sequence or a light chain variable sequence that isat least 75% (e.g., 80%, 85%, 90%, 95%, 98%, or 99%) identical to theheavy chain variable sequence and/or any light chain variable sequenceof any anti-transferrin receptor antibody, such as any one of theanti-transferrin receptor antibodies selected from Table 1. In someembodiments, the homologous heavy chain variable and/or a light chainvariable amino acid sequences do not vary within any of the CDRsequences provided herein. For example, in some embodiments, the degreeof sequence variation (e.g., 75%, 80%, 85%, 90%, 95%, 98%, or 99%) mayoccur within a heavy chain variable and/or a light chain variablesequence excluding any of the CDR sequences provided herein. In someembodiments, any of the anti-transferrin receptor antibodies providedherein comprise a heavy chain variable sequence and a light chainvariable sequence that comprises a framework sequence that is at least75%, 80%, 85%, 90%, 95%, 98%, or 99% identical to the framework sequenceof any anti-transferrin receptor antibody, such as any one of theanti-transferrin receptor antibodies selected from Table 1.

In some embodiments, an anti-transferrin receptor antibody, whichspecifically binds to transferrin receptor (e.g., human transferrinreceptor), comprises a light chain variable VL domain comprising any ofthe CDR-L domains (CDR-L1, CDR-L2, and CDR-L3), or CDR-L domain variantsprovided herein, of any of the anti-transferrin receptor antibodiesselected from Table 1. In some embodiments, an anti-transferrin receptorantibody, which specifically binds to transferrin receptor (e.g., humantransferrin receptor), comprises a light chain variable VL domaincomprising the CDR-L1, the CDR-L2, and the CDR-L3 of anyanti-transferrin receptor antibody, such as any one of theanti-transferrin receptor antibodies selected from Table 1. In someembodiments, the anti-transferrin receptor antibody comprises a lightchain variable (VL) region sequence comprising one, two, three or fourof the framework regions of the light chain variable region sequence ofany anti-transferrin receptor antibody, such as any one of theanti-transferrin receptor antibodies selected from Table 1. In someembodiments, the anti-transferrin receptor antibody comprises one, two,three or four of the framework regions of a light chain variable regionsequence which is at least 75%, 80%, 85%, 90%, 95%, or 100% identical toone, two, three or four of the framework regions of the light chainvariable region sequence of any anti-transferrin receptor antibody, suchas any one of the anti-transferrin receptor antibodies selected fromTable 1. In some embodiments, the light chain variable framework regionthat is derived from said amino acid sequence consists of said aminoacid sequence but for the presence of up to 10 amino acid substitutions,deletions, and/or insertions, preferably up to 10 amino acidsubstitutions. In some embodiments, the light chain variable frameworkregion that is derived from said amino acid sequence consists of saidamino acid sequence with 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 amino acidresidues being substituted for an amino acid found in an analogousposition in a corresponding non-human, primate, or human light chainvariable framework region.

In some embodiments, an anti-transferrin receptor antibody thatspecifically binds to transferrin receptor comprises the CDR-L1, theCDR-L2, and the CDR-L3 of any anti-transferrin receptor antibody, suchas any one of the anti-transferrin receptor antibodies selected fromTable 1. In some embodiments, the antibody further comprises one, two,three or all four VL framework regions derived from the VL of a human orprimate antibody. The primate or human light chain framework region ofthe antibody selected for use with the light chain CDR sequencesdescribed herein, can have, for example, at least 70% (e.g., at least75%, 80%, 85%, 90%, 95%, 98%, or at least 99%) identity with a lightchain framework region of a non-human parent antibody. The primate orhuman antibody selected can have the same or substantially the samenumber of amino acids in its light chain complementarity determiningregions to that of the light chain complementarity determining regionsof any of the antibodies provided herein, e.g., any of theanti-transferrin receptor antibodies selected from Table 1. In someembodiments, the primate or human light chain framework region aminoacid residues are from a natural primate or human antibody light chainframework region having at least 75% identity, at least 80% identity, atleast 85% identity, at least 90% identity, at least 95% identity, atleast 98% identity, at least 99% (or more) identity with the light chainframework regions of any anti-transferrin receptor antibody, such as anyone of the anti-transferrin receptor antibodies selected from Table 1.In some embodiments, an anti-transferrin receptor antibody furthercomprises one, two, three or all four VL framework regions derived froma human light chain variable kappa subfamily. In some embodiments, ananti-transferrin receptor antibody further comprises one, two, three orall four VL framework regions derived from a human light chain variablelambda subfamily.

In some embodiments, any of the anti-transferrin receptor antibodiesprovided herein comprise a light chain variable domain that furthercomprises a light chain constant region. In some embodiments, the lightchain constant region is a kappa, or a lambda light chain constantregion. In some embodiments, the kappa or lambda light chain constantregion is from a mammal, e.g., from a human, monkey, rat, or mouse. Insome embodiments, the light chain constant region is a human kappa lightchain constant region. In some embodiments, the light chain constantregion is a human lambda light chain constant region. It should beappreciated that any of the light chain constant regions provided hereinmay be variants of any of the light chain constant regions providedherein. In some embodiments, the light chain constant region comprisesan amino acid sequence that is at least 75%, 80%, 85%, 90%, 95%, 98%, or99% identical to any of the light chain constant regions of anyanti-transferrin receptor antibody, such as any one of theanti-transferrin receptor antibodies selected from Table 1.

In some embodiments, the anti-transferrin receptor antibody is anyanti-transferrin receptor antibody, such as any one of theanti-transferrin receptor antibodies selected from Table 1.

In some embodiments, an anti-transferrin receptor antibody comprises aVL domain comprising the amino acid sequence of any anti-transferrinreceptor antibody, such as any one of the anti-transferrin receptorantibodies selected from Table 1, and wherein the constant regionscomprise the amino acid sequences of the constant regions of an IgG,IgE, IgM, IgD, IgA or IgY immunoglobulin molecule, or a human IgG, IgE,IgM, IgD, IgA or IgY immunoglobulin molecule. In some embodiments, ananti-transferrin receptor antibody comprises any of the VL domains, orVL domain variants, and any of the VH domains, or VH domain variants,wherein the VL and VH domains, or variants thereof, are from the sameantibody clone, and wherein the constant regions comprise the amino acidsequences of the constant regions of an IgG, IgE, IgM, IgD, IgA or IgYimmunoglobulin molecule, any class (e.g., IgG1, IgG2, IgG3, IgG4, IgA1and IgA2), or any subclass (e.g., IgG2a and IgG2b) of immunoglobulinmolecule. Non-limiting examples of human constant regions are describedin the art, e.g., see Kabat E A et al., (1991) supra.

In some embodiments, an antibody of the disclosure can bind to a targetantigen (e.g., transferrin receptor) with relatively high affinity,e.g., with a K_(D) less than 10⁻⁶ M, 10⁻⁷ M, 10⁻⁸M, 10⁻⁹M, 10⁻¹⁰ M,10⁻¹¹ M or lower. For example, anti-transferrin receptor antibodies canbind to a transferrin receptor protein (e.g., human transferrinreceptor) with an affinity between 5 pM and 500 nM, e.g., between 50 pMand 100 nM, e.g., between 500 pM and 50 nM. The disclosure also includesantibodies that compete with any of the antibodies described herein forbinding to a transferrin receptor protein (e.g., human transferrinreceptor) and that have an affinity of 50 nM or lower (e.g., 20 nM orlower, 10 nM or lower, 500 pM or lower, 50 pM or lower, or 5 pM orlower). The affinity and binding kinetics of the anti-transferrinreceptor antibody can be tested using any suitable method including butnot limited to biosensor technology (e.g., OCTET or BIACORE).

In some embodiments, an antibody of the disclosure can bind to a targetantigen (e.g., transferrin receptor) with relatively high affinity,e.g., with a K_(D) less than 10⁻⁶ M, 10⁻⁷ M, 10⁻⁸M, 10⁻⁹M, 10⁻¹⁰ M,10⁻¹¹ M or lower. For example, anti-transferrin receptor antibodies canbind to a transferrin receptor protein (e.g., human transferrinreceptor) with an affinity between 5 pM and 500 nM, e.g., between 50 pMand 100 nM, e.g., between 500 pM and 50 nM. The disclosure also includesantibodies that compete with any of the antibodies described herein forbinding to a transferrin receptor protein (e.g., human transferrinreceptor) and that have an affinity of 50 nM or lower (e.g., 20 nM orlower, 10 nM or lower, 500 pM or lower, 50 pM or lower, or 5 pM orlower). The affinity and binding kinetics of the anti-transferrinreceptor antibody can be tested using any suitable method including butnot limited to biosensor technology (e.g., OCTET or BIACORE).

In some embodiments, the muscle-targeting agent is a transferrinreceptor antibody (e.g., the antibody and variants thereof as describedin International Application Publication WO 2016/081643, incorporatedherein by reference).

The heavy chain and light chain CDRs of the antibody according todifferent definition systems are provided in Table 1.1. The differentdefinition systems, e.g., the Kabat definition, the Chothia definition,and/or the contact definition have been described. See, e.g., (e.g.,Kabat, E. A., et al. (1991) Sequences of Proteins of ImmunologicalInterest, Fifth Edition, U.S. Department of Health and Human Services,NIH Publication No. 91-3242, Chothia et al., (1989) Nature 342:877;Chothia, C. et al. (1987) J. Mol. Biol. 196:901-917, Al-lazikani et al(1997) J. Molec. Biol. 273:927-948; and Almagro, J. Mol. Recognit.17:132-143 (2004). See also hgmp.mrc.ac.uk and bioinf.org.uk/abs).

TABLE 1.1 Heavy chain and light chain CDRsof a mouse transferrin receptor antibody CDRs Kabat Chothia ContactCDR-H1 SYWMH GYTFTSY TSYWMH (SEQ ID (SEQ ID (SEQ ID NO: 17) NO: 23)NO: 25) CDR-H2 EINPTNG NPTNGR WIGEINP RTNYIEK (SEQ ID TNGRTN FKS NO: 24)(SEQ ID (SEQ ID NO: 26) NO: 18) CDR-H3 GTRAYHY GTRAYHY ARGTRA (SEQ ID(SEQ ID (SEQ ID NO: 19) NO: 19) NO: 27) CDR-L1 RASDNL RASDNLYSNLAYSNLAWY YSNLA (SEQ ID (SEQ ID (SEQ ID NO: 20) NO: 28) NO: 20) CDR-L2DATNLAD DATNLAD LLVYDAT NLA (SEQ ID (SEQ ID (SEQ ID NO: 21) NO: 21)NO: 29) CDR-L3 QHFWGT QHFWGT QHFWGT PLT PLT PL (SEQ ID (SEQ ID (SEQ IDNO: 22) NO: 22) NO: 30)

The heavy chain variable domain (VH) and light chain variable domainsequences are also provided:

VH (SEQ ID NO: 33) QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGQGLEWIGEINPTNGRTNYIEKFKSKATLTVDKSSSTAYMQLSSLTSEDSAVYYCARGTRAYHYWGQGTSVTVSS VL (SEQ ID NO: 34)DIQMTQSPASLSVSVGETVTITCRASDNLYSNLAWYQQKQGKSPQLLVYDATNLADGVPSRFSGSGSGTQYSLKINSLQSEDFGTY YCQHFWGTPLTFGAGTKLELK

In some embodiments, the transferrin receptor antibody of the presentdisclosure comprises a CDR-H1, a CDR-H2, and a CDR-H3 that are the sameas the CDR-H1, CDR-H2, and CDR-H3 shown in Table 1.1. Alternatively orin addition, the transferrin receptor antibody of the present disclosurecomprises a CDR-L1, a CDR-L2, and a CDR-L3 that are the same as theCDR-L1, CDR-L2, and CDR-L3 shown in Table 1.1.

In some embodiments, the transferrin receptor antibody of the presentdisclosure comprises a CDR-H1, a CDR-H2, and a CDR-H3, whichcollectively contains no more than 5 amino acid variations (e.g., nomore than 5, 4, 3, 2, or 1 amino acid variation) as compared with theCDR-H1, CDR-H2, and CDR-H3 as shown in Table 1.1. “Collectively” meansthat the total number of amino acid variations in all of the three heavychain CDRs is within the defined range. Alternatively or in addition,the transferrin receptor antibody of the present disclosure may comprisea CDR-L1, a CDR-L2, and a CDR-L3, which collectively contains no morethan 5 amino acid variations (e.g., no more than 5, 4, 3, 2 or 1 aminoacid variation) as compared with the CDR-L1, CDR-L2, and CDR-L3 as shownin Table 1.1.

In some embodiments, the transferrin receptor antibody of the presentdisclosure comprises a CDR-H1, a CDR-H2, and a CDR-H3, at least one ofwhich contains no more than 3 amino acid variations (e.g., no more than3, 2, or 1 amino acid variation) as compared with the counterpart heavychain CDR as shown in Table 1.1. Alternatively or in addition, thetransferrin receptor antibody of the present disclosure may compriseCDR-L1, a CDR-L2, and a CDR-L3, at least one of which contains no morethan 3 amino acid variations (e.g., no more than 3, 2, or 1 amino acidvariation) as compared with the counterpart light chain CDR as shown inTable 1.1.

In some embodiments, the transferrin receptor antibody of the presentdisclosure comprises a CDR-L3, which contains no more than 3 amino acidvariations (e.g., no more than 3, 2, or 1 amino acid variation) ascompared with the CDR-L3 as shown in Table 1.1. In some embodiments, thetransferrin receptor antibody of the present disclosure comprises aCDR-L3 containing one amino acid variation as compared with the CDR-L3as shown in Table 1.1. In some embodiments, the transferrin receptorantibody of the present disclosure comprises a CDR-L3 of QHFAGTPLT (SEQID NO: 31 according to the Kabat and Chothia definition system) orQHFAGTPL (SEQ ID NO: 32 according to the Contact definition system). Insome embodiments, the transferrin receptor antibody of the presentdisclosure comprises a CDR-H1, a CDR-H2, a CDR-H3, a CDR-L1 and a CDR-L2that are the same as the CDR-H1, CDR-H2, and CDR-H3 shown in Table 1.1,and comprises a CDR-L3 of QHFAGTPLT (SEQ ID NO: 31 according to theKabat and Chothia definition system) or QHFAGTPL (SEQ ID NO: 32according to the Contact definition system).

In some embodiments, the transferrin receptor antibody of the presentdisclosure comprises heavy chain CDRs that collectively are at least 80%(e.g., 80%, 85%, 90%, 95%, or 98%) identical to the heavy chain CDRs asshown in Table 1.1. Alternatively or in addition, the transferrinreceptor antibody of the present disclosure comprises light chain CDRsthat collectively are at least 80% (e.g., 80%, 85%, 90%, 95%, or 98%)identical to the light chain CDRs as shown in Table 1.1.

In some embodiments, the transferrin receptor antibody of the presentdisclosure comprises a VH comprising the amino acid sequence of SEQ IDNO: 33. Alternatively or in addition, the transferrin receptor antibodyof the present disclosure comprises a VL comprising the amino acidsequence of SEQ ID NO: 34.

In some embodiments, the transferrin receptor antibody of the presentdisclosure comprises a VH containing no more than 20 amino acidvariations (e.g., no more than 20, 19, 18, 17, 16, 15, 14, 13, 12, 11,10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 amino acid variation) as compared withthe VH as set forth in SEQ ID NO: 33. Alternatively or in addition, thetransferrin receptor antibody of the present disclosure comprises a VLcontaining no more than 15 amino acid variations (e.g., no more than 20,19, 18, 17, 16, 15, 14, 13, 12, 11, 9, 8, 7, 6, 5, 4, 3, 2, or 1 aminoacid variation) as compared with the VL as set forth in SEQ ID NO: 34.

In some embodiments, the transferrin receptor antibody of the presentdisclosure comprises a VH comprising an amino acid sequence that is atleast 80% (e.g., 80%, 85%, 90%, 95%, or 98%) identical to the VH as setforth in SEQ ID NO: 33. Alternatively or in addition, the transferrinreceptor antibody of the present disclosure comprises a VL comprising anamino acid sequence that is at least 80% (e.g., 80%, 85%, 90%, 95%, or98%) identical to the VL as set forth in SEQ ID NO: 34.

In some embodiments, the transferrin receptor antibody of the presentdisclosure is a humanized antibody (e.g., a humanized variant of anantibody). In some embodiments, the transferrin receptor antibody of thepresent disclosure comprises a CDR-H1, a CDR-H2, a CDR-H3, a CDR-L1, aCDR-L2, and a CDR-L3 that are the same as the CDR-H1, CDR-H2, and CDR-H3shown in Table 1.1, and comprises a humanized heavy chain variableregion and/or a humanized light chain variable region.

Humanized antibodies are human immunoglobulins (recipient antibody) inwhich residues from a complementary determining region (CDR) of therecipient are replaced by residues from a CDR of a non-human species(donor antibody) such as mouse, rat, or rabbit having the desiredspecificity, affinity, and capacity. In some embodiments, Fv frameworkregion (FR) residues of the human immunoglobulin are replaced bycorresponding non-human residues. Furthermore, the humanized antibodymay comprise residues that are found neither in the recipient antibodynor in the imported CDR or framework sequences, but are included tofurther refine and optimize antibody performance. In general, thehumanized antibody will comprise substantially all of at least one, andtypically two, variable domains, in which all or substantially all ofthe CDR regions correspond to those of a non-human immunoglobulin andall or substantially all of the FR regions are those of a humanimmunoglobulin consensus sequence. The humanized antibody optimally alsowill comprise at least a portion of an immunoglobulin constant region ordomain (Fc), typically that of a human immunoglobulin. Antibodies mayhave Fc regions modified as described in WO 99/58572. Other forms ofhumanized antibodies have one or more CDRs (one, two, three, four, five,six) which are altered with respect to the original antibody, which arealso termed one or more CDRs derived from one or more CDRs from theoriginal antibody. Humanized antibodies may also involve affinitymaturation.

In some embodiments, humanization is achieved by grafting the CDRs(e.g., as shown in Table 1.1) into the IGKV1-NL1*01 and IGHV1-3*01 humanvariable domains. In some embodiments, the transferrin receptor antibodyof the present disclosure is a humanized variant comprising one or moreamino acid substitutions at positions 9, 13, 17, 18, 40, 45, and 70 ascompared with the VL as set forth in SEQ ID NO: 34, and/or one or moreamino acid substitutions at positions 1, 5, 7, 11, 12, 20, 38, 40, 44,66, 75, 81, 83, 87, and 108 as compared with the VH as set forth in SEQID NO: 33. In some embodiments, the transferrin receptor antibody of thepresent disclosure is a humanized variant comprising amino acidsubstitutions at all of positions 9, 13, 17, 18, 40, 45, and 70 ascompared with the VL as set forth in SEQ ID NO: 34, and/or amino acidsubstitutions at all of positions 1, 5, 7, 11, 12, 20, 38, 40, 44, 66,75, 81, 83, 87, and 108 as compared with the VH as set forth in SEQ IDNO: 33.

In some embodiments, the transferrin receptor antibody of the presentdisclosure is a humanized antibody and contains the residues atpositions 43 and 48 of the VL as set forth in SEQ ID NO: 34.Alternatively or in addition, the transferrin receptor antibody of thepresent disclosure is a humanized antibody and contains the residues atpositions 48, 67, 69, 71, and 73 of the VH as set forth in SEQ ID NO:33.

The VH and VL amino acid sequences of an example humanized antibody thatmay be used in accordance with the present disclosure are provided:

Humanized VH (SEQ ID NO: 35) EVQLVQSGAEVKKPGASVKVSCKASGYTFTSYWMHWVRQAPGQRLEWIGEINPTNGRTNYIEKFKSRATLTVDKSASTAYMELSSLRSEDTAVYYCARGTRAYHYWGQGTMVTVSS Humanized VL (SEQ ID NO: 36)DIQMTQSPSSLSASVGDRVTITCRASDNLYSNLAWYQQKPGKSPKLLVYDATNLADGVPSRFSGSGSGTDYSLKINSLQSEDFGTY YCQHFWGTPLTFGAGTKLELK

In some embodiments, the transferrin receptor antibody of the presentdisclosure comprises a VH comprising the amino acid sequence of SEQ IDNO: 35. Alternatively or in addition, the transferrin receptor antibodyof the present disclosure comprises a VL comprising the amino acidsequence of SEQ ID NO: 36.

In some embodiments, the transferrin receptor antibody of the presentdisclosure comprises a VH containing no more than 20 amino acidvariations (e.g., no more than 20, 19, 18, 17, 16, 15, 14, 13, 12, 11,10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 amino acid variation) as compared withthe VH as set forth in SEQ ID NO: 35. Alternatively or in addition, thetransferrin receptor antibody of the present disclosure comprises a VLcontaining no more than 15 amino acid variations (e.g., no more than 20,19, 18, 17, 16, 15, 14, 13, 12, 11, 9, 8, 7, 6, 5, 4, 3, 2, or 1 aminoacid variation) as compared with the VL as set forth in SEQ ID NO: 36.

In some embodiments, the transferrin receptor antibody of the presentdisclosure comprises a VH comprising an amino acid sequence that is atleast 80% (e.g., 80%, 85%, 90%, 95%, or 98%) identical to the VH as setforth in SEQ ID NO: 35. Alternatively or in addition, the transferrinreceptor antibody of the present disclosure comprises a VL comprising anamino acid sequence that is at least 80% (e.g., 80%, 85%, 90%, 95%, or98%) identical to the VL as set forth in SEQ ID NO: 36.

In some embodiments, the transferrin receptor antibody of the presentdisclosure is a humanized variant comprising amino acid substitutions atone or more of positions 43 and 48 as compared with the VL as set forthin SEQ ID NO: 34, and/or amino acid substitutions at one or more ofpositions 48, 67, 69, 71, and 73 as compared with the VH as set forth inSEQ ID NO: 33. In some embodiments, the transferrin receptor antibody ofthe present disclosure is a humanized variant comprising a S43A and/or aV48L mutation as compared with the VL as set forth in SEQ ID NO: 34,and/or one or more of A67V, L69I, V71R, and K73T mutations as comparedwith the VH as set forth in SEQ ID NO: 33

In some embodiments, the transferrin receptor antibody of the presentdisclosure is a humanized variant comprising amino acid substitutions atone or more of positions 9, 13, 17, 18, 40, 43, 48, 45, and 70 ascompared with the VL as set forth in SEQ ID NO: 34, and/or amino acidsubstitutions at one or more of positions 1, 5, 7, 11, 12, 20, 38, 40,44, 48, 66, 67, 69, 71, 73, 75, 81, 83, 87, and 108 as compared with theVH as set forth in SEQ ID NO: 33.

In some embodiments, the transferrin receptor antibody of the presentdisclosure is a chimeric antibody, which can include a heavy constantregion and a light constant region from a human antibody. Chimericantibodies refer to antibodies having a variable region or part ofvariable region from a first species and a constant region from a secondspecies. Typically, in these chimeric antibodies, the variable region ofboth light and heavy chains mimics the variable regions of antibodiesderived from one species of mammals (e.g., a non-human mammal such asmouse, rabbit, and rat), while the constant portions are homologous tothe sequences in antibodies derived from another mammal such as human.In some embodiments, amino acid modifications can be made in thevariable region and/or the constant region.

In some embodiments, the transferrin receptor antibody described hereinis a chimeric antibody, which can include a heavy constant region and alight constant region from a human antibody. Chimeric antibodies referto antibodies having a variable region or part of variable region from afirst species and a constant region from a second species. Typically, inthese chimeric antibodies, the variable region of both light and heavychains mimics the variable regions of antibodies derived from onespecies of mammals (e.g., a non-human mammal such as mouse, rabbit, andrat), while the constant portions are homologous to the sequences inantibodies derived from another mammal such as human. In someembodiments, amino acid modifications can be made in the variable regionand/or the constant region.

In some embodiments, the heavy chain of any of the transferrin receptorantibodies as described herein may comprises a heavy chain constantregion (CH) or a portion thereof (e.g., CH1, CH2, CH3, or a combinationthereof). The heavy chain constant region can of any suitable origin,e.g., human, mouse, rat, or rabbit. In one specific example, the heavychain constant region is from a human IgG (a gamma heavy chain), e.g.,IgG1, IgG2, or IgG4. An exemplary human IgG1 constant region is givenbelow:

(SEQ ID NO: 37) ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK

In some embodiments, the light chain of any of the transferrin receptorantibodies described herein may further comprise a light chain constantregion (CL), which can be any CL known in the art. In some examples, theCL is a kappa light chain. In other examples, the CL is a lambda lightchain. In some embodiments, the CL is a kappa light chain, the sequenceof which is provided below:

(SEQ ID NO: 38) ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVN HKPSNTKVDKKVEPKSCDKTHTCP

Other antibody heavy and light chain constant regions are well known inthe art, e.g., those provided in the IMGT database (www.imgt.org) or atwww.vbase2.org/vbstat.php., both of which are incorporated by referenceherein.

Exemplary heavy chain and light chain amino acid sequences of thetransferrin receptor antibodies described are provided below:

Heavy Chain (VH + human IgG1 constant region) (SEQ ID NO: 39)QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGQGLEWIGEINPTNGRTNYIEKFKSKATLTVDKSSSTAYMQLSSLTSEDSAVYYCARGTRAYHYWGQGTSVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSL SLSPGKLight Chain (VL + kappa light chain) (SEQ ID NO: 40)QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGQGLEWIGEINPTNGRTNYIEKFKSKATLTVDKSSSTAYMQLSSLTSEDSAVYYCARGTRAYHYWGQGTSVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCP Heavy Chain (humanized VH + human IgG1constant region) (SEQ ID NO: 41)EVQLVQSGAEVKKPGASVKVSCKASGYTFTSYWMHWVRQAPGQRLEWIGEINPTNGRTNYIEKFKSRATLTVDKSASTAYMELSSLRSEDTAVYYCARGTRAYHYWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGKLight Chain (humanized VL + kappa light chain) (SEQ ID NO: 42)DIQMTQSPSSLSASVGDRVTITCRASDNLYSNLAWYQQKPGKSPKLLVYDATNLADGVPSRFSGSGSGTDYSLKINSLQSEDFGTYYCQHFWGTPLTFGAGTKLELKASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTK VDKKVEPKSCDKTHTCP

In some embodiments, the transferrin receptor antibody described hereincomprises a heavy chain comprising an amino acid sequence that is atleast 80% (e.g., 80%, 85%, 90%, 95%, or 98%) identical to SEQ ID NO: 39.Alternatively or in addition, the transferrin receptor antibodydescribed herein comprises a light chain comprising an amino acidsequence that is at least 80% (e.g., 80%, 85%, 90%, 95%, or 98%)identical to SEQ ID NO: 40. In some embodiments, the transferrinreceptor antibody described herein comprises a heavy chain comprisingthe amino acid sequence of SEQ ID NO: 39. Alternatively or in addition,the transferrin receptor antibody described herein comprises a lightchain comprising the amino acid sequence of SEQ ID NO: 40.

In some embodiments, the transferrin receptor antibody of the presentdisclosure comprises a heavy chain containing no more than 20 amino acidvariations (e.g., no more than 20, 19, 18, 17, 16, 15, 14, 13, 12, 11,10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 amino acid variation) as compared withthe heavy chain as set forth in SEQ ID NO: 39. Alternatively or inaddition, the transferrin receptor antibody of the present disclosurecomprises a light chain containing no more than 15 amino acid variations(e.g., no more than 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 9, 8, 7, 6,5, 4, 3, 2, or 1 amino acid variation) as compared with the light chainas set forth in SEQ ID NO: 40.

In some embodiments, the transferrin receptor antibody described hereincomprises a heavy chain comprising an amino acid sequence that is atleast 80% (e.g., 80%, 85%, 90%, 95%, or 98%) identical to SEQ ID NO: 41.Alternatively or in addition, the transferrin receptor antibodydescribed herein comprises a light chain comprising an amino acidsequence that is at least 80% (e.g., 80%, 85%, 90%, 95%, or 98%)identical to SEQ ID NO: 42. In some embodiments, the transferrinreceptor antibody described herein comprises a heavy chain comprisingthe amino acid sequence of SEQ ID NO: 41. Alternatively or in addition,the transferrin receptor antibody described herein comprises a lightchain comprising the amino acid sequence of SEQ ID NO: 42.

In some embodiments, the transferrin receptor antibody of the presentdisclosure comprises a heavy chain containing no more than 20 amino acidvariations (e.g., no more than 20, 19, 18, 17, 16, 15, 14, 13, 12, 11,10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 amino acid variation) as compared withthe heavy chain of humanized antibody as set forth in SEQ ID NO: 39.Alternatively or in addition, the transferrin receptor antibody of thepresent disclosure comprises a light chain containing no more than 15amino acid variations (e.g., no more than 20, 19, 18, 17, 16, 15, 14,13, 12, 11, 9, 8, 7, 6, 5, 4, 3, 2, or 1 amino acid variation) ascompared with the light chain of humanized antibody as set forth in SEQID NO: 40.

In some embodiments, the transferrin receptor antibody is an antigenbinding fragment (FAB) of an intact antibody (full-length antibody).Antigen binding fragment of an intact antibody (full-length antibody)can be prepared via routine methods. For example, F(ab′)2 fragments canbe produced by pepsin digestion of an antibody molecule, and Fabfragments that can be generated by reducing the disulfide bridges ofF(ab′)2 fragments. Exemplary FABs amino acid sequences of thetransferrin receptor antibodies described herein are provided below:

Heavy Chain FAB (VH + a portion of human IgG1 constant region)(SEQ ID NO: 43) QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGQGLEWIGEINPTNGRTNYIEKFKSKATLTVDKSSSTAYMQLSSLTSEDSAVYYCARGTRAYHYWGQGTSVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCP Heavy Chain FAB (humanized VH + a portion ofhuman IgG1 constant region) (SEQ ID NO: 44)EVQLVQSGAEVKKPGASVKVSCKASGYTFTSYWMHWVRQAPGQRLEWIGEINPTNGRTNYIEKFKSRATLTVDKSASTAYMELSSLRSEDTAVYYCARGTRAYHYWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCP

The transferrin receptor antibodies described herein can be in anyantibody form, including, but not limited to, intact (i.e., full-length)antibodies, antigen-binding fragments thereof (such as Fab, Fab′,F(ab′)2, Fv), single chain antibodies, bi-specific antibodies, ornanobodies. In some embodiments, the transferrin receptor antibodydescribed herein is a scFv. In some embodiments, the transferrinreceptor antibody described herein is a scFv-Fab (e.g., scFv fused to aportion of a constant region). In some embodiments, the transferrinreceptor antibody described herein is a scFv fused to a constant region(e.g., human IgG1 constant region as set forth in SEQ ID NO: 39).

b. Other Muscle-Targeting Antibodies

In some embodiments, the muscle-targeting antibody is an antibody thatspecifically binds hemojuvelin, caveolin-3, Duchenne muscular dystrophypeptide, myosin Iib, or CD63. In some embodiments, the muscle-targetingantibody is an antibody that specifically binds a myogenic precursorprotein. Exemplary myogenic precursor proteins include, withoutlimitation, ABCG2, M-Cadherin/Cadherin-15, Caveolin-1, CD34, FoxK1,Integrin alpha 7, Integrin alpha 7 beta 1, MYF-5, MyoD, Myogenin,NCAM-1/CD56, Pax3, Pax7, and Pax9. In some embodiments, themuscle-targeting antibody is an antibody that specifically binds askeletal muscle protein. Exemplary skeletal muscle proteins include,without limitation, alpha-Sarcoglycan, beta-Sarcoglycan, CalpainInhibitors, Creatine Kinase MM/CKMM, eIF5A, Enolase 2/Neuron-specificEnolase, epsilon-Sarcoglycan, FABP3/H-FABP, GDF-8/Myostatin,GDF-11/GDF-8, Integrin alpha 7, Integrin alpha 7 beta 1, Integrin beta1/CD29, MCAM/CD146, MyoD, Myogenin, Myosin Light Chain KinaseInhibitors, NCAM-1/CD56, and Troponin I. In some embodiments, themuscle-targeting antibody is an antibody that specifically binds asmooth muscle protein. Exemplary smooth muscle proteins include, withoutlimitation, alpha-Smooth Muscle Actin, VE-Cadherin, Caldesmon/CALD1,Calponin 1, Desmin, Histamine H2 R, Motilin R/GPR38, Transgelin/TAGLN,and Vimentin. However, it should be appreciated that antibodies toadditional targets are within the scope of this disclosure and theexemplary lists of targets provided herein are not meant to be limiting.

c. Antibody Features/Alterations

In some embodiments, conservative mutations can be introduced intoantibody sequences (e.g., CDRs or framework sequences) at positionswhere the residues are not likely to be involved in interacting with atarget antigen (e.g., transferrin receptor), for example, as determinedbased on a crystal structure. In some embodiments, one, two or moremutations (e.g., amino acid substitutions) are introduced into the Fcregion of a muscle-targeting antibody described herein (e.g., in a CH2domain (residues 231-340 of human IgG1) and/or CH3 domain (residues341-447 of human IgG1) and/or the hinge region, with numbering accordingto the Kabat numbering system (e.g., the EU index in Kabat)) to alterone or more functional properties of the antibody, such as serumhalf-life, complement fixation, Fc receptor binding and/orantigen-dependent cellular cytotoxicity.

In some embodiments, one, two or more mutations (e.g., amino acidsubstitutions) are introduced into the hinge region of the Fc region(CH1 domain) such that the number of cysteine residues in the hingeregion are altered (e.g., increased or decreased) as described in, e.g.,U.S. Pat. No. 5,677,425. The number of cysteine residues in the hingeregion of the CH1 domain can be altered to, e.g., facilitate assembly ofthe light and heavy chains, or to alter (e.g., increase or decrease) thestability of the antibody or to facilitate linker conjugation.

In some embodiments, one, two or more mutations (e.g., amino acidsubstitutions) are introduced into the Fc region of a muscle-targetingantibody described herein (e.g., in a CH2 domain (residues 231-340 ofhuman IgG1) and/or CH3 domain (residues 341-447 of human IgG1) and/orthe hinge region, with numbering according to the Kabat numbering system(e.g., the EU index in Kabat)) to increase or decrease the affinity ofthe antibody for an Fc receptor (e.g., an activated Fc receptor) on thesurface of an effector cell. Mutations in the Fc region of an antibodythat decrease or increase the affinity of an antibody for an Fc receptorand techniques for introducing such mutations into the Fc receptor orfragment thereof are known to one of skill in the art. Examples ofmutations in the Fc receptor of an antibody that can be made to alterthe affinity of the antibody for an Fc receptor are described in, e.g.,Smith P et al., (2012) PNAS 109: 6181-6186, U.S. Pat. No. 6,737,056, andInternational Publication Nos. WO 02/060919; WO 98/23289; and WO97/34631, which are incorporated herein by reference.

In some embodiments, one, two or more amino acid mutations (i.e.,substitutions, insertions or deletions) are introduced into an IgGconstant domain, or FcRn-binding fragment thereof (preferably an Fc orhinge-Fc domain fragment) to alter (e.g., decrease or increase)half-life of the antibody in vivo. See, e.g., International PublicationNos. WO 02/060919; WO 98/23289; and WO 97/34631; and U.S. Pat. Nos.5,869,046, 6,121,022, 6,277,375 and 6,165,745 for examples of mutationsthat will alter (e.g., decrease or increase) the half-life of anantibody in vivo.

In some embodiments, one, two or more amino acid mutations (i.e.,substitutions, insertions or deletions) are introduced into an IgGconstant domain, or FcRn-binding fragment thereof (preferably an Fc orhinge-Fc domain fragment) to decrease the half-life of theanti-transferrin receptor antibody in vivo. In some embodiments, one,two or more amino acid mutations (i.e., substitutions, insertions ordeletions) are introduced into an IgG constant domain, or FcRn-bindingfragment thereof (preferably an Fc or hinge-Fc domain fragment) toincrease the half-life of the antibody in vivo. In some embodiments, theantibodies can have one or more amino acid mutations (e.g.,substitutions) in the second constant (CH2) domain (residues 231-340 ofhuman IgG1) and/or the third constant (CH3) domain (residues 341-447 ofhuman IgG1), with numbering according to the EU index in Kabat (Kabat EA et al., (1991) supra). In some embodiments, the constant region of theIgG1 of an antibody described herein comprises a methionine (M) totyrosine (Y) substitution in position 252, a serine (S) to threonine (T)substitution in position 254, and a threonine (T) to glutamic acid (E)substitution in position 256, numbered according to the EU index as inKabat. See U.S. Pat. No. 7,658,921, which is incorporated herein byreference. This type of mutant IgG, referred to as “YTE mutant” has beenshown to display fourfold increased half-life as compared to wild-typeversions of the same antibody (see Dall'Acqua W F et al., (2006) J BiolChem 281: 23514-24). In some embodiments, an antibody comprises an IgGconstant domain comprising one, two, three or more amino acidsubstitutions of amino acid residues at positions 251-257, 285-290,308-314, 385-389, and 428-436, numbered according to the EU index as inKabat.

In some embodiments, one, two or more amino acid substitutions areintroduced into an IgG constant domain Fc region to alter the effectorfunction(s) of the anti-transferrin receptor antibody. The effectorligand to which affinity is altered can be, for example, an Fc receptoror the Cl component of complement. This approach is described in furtherdetail in U.S. Pat. Nos. 5,624,821 and 5,648,260. In some embodiments,the deletion or inactivation (through point mutations or other means) ofa constant region domain can reduce Fc receptor binding of thecirculating antibody thereby increasing tumor localization. See, e.g.,U.S. Pat. Nos. 5,585,097 and 8,591,886 for a description of mutationsthat delete or inactivate the constant domain and thereby increase tumorlocalization. In some embodiments, one or more amino acid substitutionsmay be introduced into the Fc region of an antibody described herein toremove potential glycosylation sites on Fc region, which may reduce Fcreceptor binding (see, e.g., Shields R L et al., (2001) J Biol Chem 276:6591-604).

In some embodiments, one or more amino in the constant region of amuscle-targeting antibody described herein can be replaced with adifferent amino acid residue such that the antibody has altered Clqbinding and/or reduced or abolished complement dependent cytotoxicity(CDC). This approach is described in further detail in U.S. Pat. No.6,194,551 (Idusogie et al). In some embodiments, one or more amino acidresidues in the N-terminal region of the CH2 domain of an antibodydescribed herein are altered to thereby alter the ability of theantibody to fix complement. This approach is described further inInternational Publication No. WO 94/29351. In some embodiments, the Fcregion of an antibody described herein is modified to increase theability of the antibody to mediate antibody dependent cellularcytotoxicity (ADCC) and/or to increase the affinity of the antibody foran Fcγ receptor. This approach is described further in InternationalPublication No. WO 00/42072.

In some embodiments, the heavy and/or light chain variable domain(s)sequence(s) of the antibodies provided herein can be used to generate,for example, CDR-grafted, chimeric, humanized, or composite humanantibodies or antigen-binding fragments, as described elsewhere herein.As understood by one of ordinary skill in the art, any variant,CDR-grafted, chimeric, humanized, or composite antibodies derived fromany of the antibodies provided herein may be useful in the compositionsand methods described herein and will maintain the ability tospecifically bind transferrin receptor, such that the variant,CDR-grafted, chimeric, humanized, or composite antibody has at least50%, at least 60%, at least 70%, at least 80%, at least 90%, at least95% or more binding to transferrin receptor relative to the originalantibody from which it is derived.

In some embodiments, the antibodies provided herein comprise mutationsthat confer desirable properties to the antibodies. For example, toavoid potential complications due to Fab-arm exchange, which is known tooccur with native IgG4 mAbs, the antibodies provided herein may comprisea stabilizing ‘Adair’ mutation (Angal S., et al., “A single amino acidsubstitution abolishes the heterogeneity of chimeric mouse/human (IgG4)antibody,” Mol Immunol 30, 105-108; 1993), where serine 228 (EUnumbering; residue 241 Kabat numbering) is converted to prolineresulting in an IgG1-like hinge sequence. Accordingly, any of theantibodies may include a stabilizing ‘Adair’ mutation.

As provided herein, antibodies of this disclosure may optionallycomprise constant regions or parts thereof. For example, a VL domain maybe attached at its C-terminal end to a light chain constant domain likeCκ or Cλ. Similarly, a VH domain or portion thereof may be attached toall or part of a heavy chain like IgA, IgD, IgE, IgG, and IgM, and anyisotype subclass. Antibodies may include suitable constant regions (see,for example, Kabat et al., Sequences of Proteins of ImmunologicalInterest, No. 91-3242, National Institutes of Health Publications,Bethesda, Md. (1991)). Therefore, antibodies within the scope of thismay disclosure include VH and VL domains, or an antigen binding portionthereof, combined with any suitable constant regions.

ii. Muscle-Targeting Peptides

Some aspects of the disclosure provide muscle-targeting peptides asmuscle-targeting agents. Short peptide sequences (e.g., peptidesequences of 5-20 amino acids in length) that bind to specific celltypes have been described. For example, cell-targeting peptides havebeen described in Vines e., et al., A. “Cell-penetrating andcell-targeting peptides in drug delivery” Biochim Biophys Acta 2008,1786: 126-38; Jarver P., et al., “In vivo biodistribution and efficacyof peptide mediated delivery” Trends Pharmacol Sci 2010; 31: 528-35;Samoylova T. I., et al., “Elucidation of muscle-binding peptides byphage display screening” Muscle Nerve 1999; 22: 460-6; U.S. Pat. No.6,329,501, issued on Dec. 11, 2001, entitled “METHODS AND COMPOSITIONSFOR TARGETING COMPOUNDS TO MUSCLE”; and Samoylov A. M., et al.,“Recognition of cell-specific binding of phage display derived peptidesusing an acoustic wave sensor.” Biomol Eng 2002; 18: 269-72; the entirecontents of each of which are incorporated herein by reference. Bydesigning peptides to interact with specific cell surface antigens(e.g., receptors), selectivity for a desired tissue, e.g., muscle, canbe achieved. Skeletal muscle-targeting has been investigated and a rangeof molecular payloads are able to be delivered. These approaches mayhave high selectivity for muscle tissue without many of the practicaldisadvantages of a large antibody or viral particle. Accordingly, insome embodiments, the muscle-targeting agent is a muscle-targetingpeptide that is from 4 to 50 amino acids in length. In some embodiments,the muscle-targeting peptide is 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or50 amino acids in length. Muscle-targeting peptides can be generatedusing any of several methods, such as phage display.

In some embodiments, a muscle-targeting peptide may bind to aninternalizing cell surface receptor that is overexpressed or relativelyhighly expressed in muscle cells, e.g. a transferrin receptor, comparedwith certain other cells. In some embodiments, a muscle-targetingpeptide may target, e.g., bind to, a transferrin receptor. In someembodiments, a peptide that targets a transferrin receptor may comprisea segment of a naturally occurring ligand, e.g., transferrin. In someembodiments, a peptide that targets a transferrin receptor is asdescribed in U.S. Pat. No. 6,743,893, filed Nov. 30, 2000,“RECEPTOR-MEDIATED UPTAKE OF PEPTIDES THAT BIND THE HUMAN TRANSFERRINRECEPTOR”. In some embodiments, a peptide that targets a transferrinreceptor is as described in Kawamoto, M. et al, “A novel transferrinreceptor-targeted hybrid peptide disintegrates cancer cell membrane toinduce rapid killing of cancer cells.” BMC Cancer. 2011 Aug. 18; 11:359.In some embodiments, a peptide that targets a transferrin receptor is asdescribed in U.S. Pat. No. 8,399,653, filed May 20, 2011,“TRANSFERRIN/TRANSFERRIN RECEPTOR-MEDIATED SIRNA DELIVERY”.

As discussed above, examples of muscle targeting peptides have beenreported. For example, muscle-specific peptides were identified usingphage display library presenting surface heptapeptides. As one example apeptide having the amino acid sequence ASSLNIA (SEQ ID NO: 6) bound toC2C12 murine myotubes in vitro, and bound to mouse muscle tissue invivo. Accordingly, in some embodiments, the muscle-targeting agentcomprises the amino acid sequence ASSLNIA (SEQ ID NO: 6). This peptidedisplayed improved specificity for binding to heart and skeletal muscletissue after intravenous injection in mice with reduced binding toliver, kidney, and brain. Additional muscle-specific peptides have beenidentified using phage display. For example, a 12 amino acid peptide wasidentified by phage display library for muscle targeting in the contextof treatment for DMD. See, Yoshida D., et al., “Targeting of salicylateto skin and muscle following topical injections in rats.” Int J Pharm2002; 231: 177-84; the entire contents of which are hereby incorporatedby reference. Here, a 12 amino acid peptide having the sequenceSKTFNTHPQSTP (SEQ ID NO: 7) was identified and this muscle-targetingpeptide showed improved binding to C2C12 cells relative to the ASSLNIA(SEQ ID NO: 6) peptide.

An additional method for identifying peptides selective for muscle(e.g., skeletal muscle) over other cell types includes in vitroselection, which has been described in Ghosh D., et al., “Selection ofmuscle-binding peptides from context-specific peptide-presenting phagelibraries for adenoviral vector targeting” J Virol 2005; 79: 13667-72;the entire contents of which are incorporated herein by reference. Bypre-incubating a random 12-mer peptide phage display library with amixture of non-muscle cell types, non-specific cell binders wereselected out. Following rounds of selection the 12 amino acid peptideTARGEHKEEELI (SEQ ID NO: 8) appeared most frequently. Accordingly, insome embodiments, the muscle-targeting agent comprises the amino acidsequence TARGEHKEEELI (SEQ ID NO: 8).

A muscle-targeting agent may an amino acid-containing molecule orpeptide. A muscle-targeting peptide may correspond to a sequence of aprotein that preferentially binds to a protein receptor found in musclecells. In some embodiments, a muscle-targeting peptide contains a highpropensity of hydrophobic amino acids, e.g. valine, such that thepeptide preferentially targets muscle cells. In some embodiments, amuscle-targeting peptide has not been previously characterized ordisclosed. These peptides may be conceived of, produced, synthesized,and/or derivatized using any of several methodologies, e.g. phagedisplayed peptide libraries, one-bead one-compound peptide libraries, orpositional scanning synthetic peptide combinatorial libraries. Exemplarymethodologies have been characterized in the art and are incorporated byreference (Gray, B. P. and Brown, K. C. “Combinatorial PeptideLibraries: Mining for Cell-Binding Peptides” Chem Rev. 2014, 114:2,1020-1081.; Samoylova, T. I. and Smith, B. F. “Elucidation ofmuscle-binding peptides by phage display screening.” Muscle Nerve, 1999,22:4. 460-6.). In some embodiments, a muscle-targeting peptide has beenpreviously disclosed (see, e.g. Writer M. J. et al. “Targeted genedelivery to human airway epithelial cells with synthetic vectorsincorporating novel targeting peptides selected by phage display.” J.Drug Targeting. 2004; 12:185; Cai, D. “BDNF-mediated enhancement ofinflammation and injury in the aging heart.” Physiol Genomics. 2006,24:3, 191-7.; Zhang, L. “Molecular profiling of heart endothelialcells.” Circulation, 2005, 112:11, 1601-11.; McGuire, M. J. et al. “Invitro selection of a peptide with high selectivity for cardiomyocytes invivo.” J Mol Biol. 2004, 342:1, 171-82.). Exemplary muscle-targetingpeptides comprise an amino acid sequence of the following group:CQAQGQLVC (SEQ ID NO: 9), CSERSMNFC (SEQ ID NO: 10), CPKTRRVPC (SEQ IDNO: 11), WLSEAGPVVTVRALRGTGSW (SEQ ID NO: 12), ASSLNIA (SEQ ID NO: 6),CMQHSMRVC (SEQ ID NO: 13), and DDTRHWG (SEQ ID NO: 14). In someembodiments, a muscle-targeting peptide may comprise about 2-25 aminoacids, about 2-20 amino acids, about 2-15 amino acids, about 2-10 aminoacids, or about 2-5 amino acids. Muscle-targeting peptides may comprisenaturally-occurring amino acids, e.g. cysteine, alanine, ornon-naturally-occurring or modified amino acids. Non-naturally occurringamino acids include β-amino acids, homo-amino acids, prolinederivatives, 3-substituted alanine derivatives, linear core amino acids,N-methyl amino acids, and others known in the art. In some embodiments,a muscle-targeting peptide may be linear; in other embodiments, amuscle-targeting peptide may be cyclic, e.g. bicyclic (see, e.g.Silvana, M. G. et al. Mol. Therapy, 2018, 26:1, 132-147.).

iii. Muscle-Targeting Receptor Ligands

A muscle-targeting agent may be a ligand, e.g. a ligand that binds to areceptor protein. A muscle-targeting ligand may be a protein, e.g.transferrin, which binds to an internalizing cell surface receptorexpressed by a muscle cell. Accordingly, in some embodiments, themuscle-targeting agent is transferrin, or a derivative thereof thatbinds to a transferrin receptor. A muscle-targeting ligand mayalternatively be a small molecule, e.g. a lipophilic small molecule thatpreferentially targets muscle cells relative to other cell types.Exemplary lipophilic small molecules that may target muscle cellsinclude compounds comprising cholesterol, cholesteryl, stearic acid,palmitic acid, oleic acid, oleyl, linolene, linoleic acid, myristicacid, sterols, dihydrotestosterone, testosterone derivatives, glycerine,alkyl chains, trityl groups, and alkoxy acids.

iv. Muscle-Targeting Aptamers

A muscle-targeting agent may be an aptamer, e.g. an RNA aptamer, whichpreferentially targets muscle cells relative to other cell types. Insome embodiments, a muscle-targeting aptamer has not been previouslycharacterized or disclosed. These aptamers may be conceived of,produced, synthesized, and/or derivatized using any of severalmethodologies, e.g. Systematic Evolution of Ligands by ExponentialEnrichment. Exemplary methodologies have been characterized in the artand are incorporated by reference (Yan, A. C. and Levy, M. “Aptamers andaptamer targeted delivery” RNA biology, 2009, 6:3, 316-20.; Germer, K.et al. “RNA aptamers and their therapeutic and diagnostic applications.”Int. J. Biochem. Mol. Biol. 2013; 4: 27-40.). In some embodiments, amuscle-targeting aptamer has been previously disclosed (see, e.g.Phillippou, S. et al. “Selection and Identification ofSkeletal-Muscle-Targeted RNA Aptamers.” Mol Ther Nucleic Acids. 2018,10:199-214.; Thiel, W. H. et al. “Smooth Muscle Cell-targeted RNAAptamer Inhibits Neointimal Formation.” Mol Ther. 2016, 24:4, 779-87.).Exemplary muscle-targeting aptamers include the A01B RNA aptamer and RNAApt 14. In some embodiments, an aptamer is a nucleic acid-based aptamer,an oligonucleotide aptamer or a peptide aptamer. In some embodiments, anaptamer may be about 5-15 kDa, about 5-10 kDa, about 10-15 kDa, about1-5 Da, about 1-3 kDa, or smaller.

v. Other Muscle-Targeting Agents

One strategy for targeting a muscle cell (e.g., a skeletal muscle cell)is to use a substrate of a muscle transporter protein, such as atransporter protein expressed on the sarcolemma. In some embodiments,the muscle-targeting agent is a substrate of an influx transporter thatis specific to muscle tissue. In some embodiments, the influxtransporter is specific to skeletal muscle tissue. Two main classes oftransporters are expressed on the skeletal muscle sarcolemma, (1) theadenosine triphosphate (ATP) binding cassette (ABC) superfamily, whichfacilitate efflux from skeletal muscle tissue and (2) the solute carrier(SLC) superfamily, which can facilitate the influx of substrates intoskeletal muscle. In some embodiments, the muscle-targeting agent is asubstrate that binds to an ABC superfamily or an SLC superfamily oftransporters. In some embodiments, the substrate that binds to the ABCor SLC superfamily of transporters is a naturally-occurring substrate.In some embodiments, the substrate that binds to the ABC or SLCsuperfamily of transporters is a non-naturally occurring substrate, forexample, a synthetic derivative thereof that binds to the ABC or SLCsuperfamily of transporters.

In some embodiments, the muscle-targeting agent is a substrate of an SLCsuperfamily of transporters. SLC transporters are either equilibrativeor use proton or sodium ion gradients created across the membrane todrive transport of substrates. Exemplary SLC transporters that have highskeletal muscle expression include, without limitation, the SATTtransporter (ASCT1; SLC1A4), GLUT4 transporter (SLC2A4), GLUT7transporter (GLUT7; SLC2A7), ATRC2 transporter (CAT-2; SLC7A2), LAT3transporter (KIAA0245; SLC7A6), PHT1 transporter (PTR4; SLC15A4), OATP-Jtransporter (OATP5A1; SLC21A15), OCT3 transporter (EMT; SLC22A3), OCTN2transporter (FLJ46769; SLC22A5), ENT transporters (ENT1; SLC29A1 andENT2; SLC29A2), PAT2 transporter (SLC36A2), and SAT2 transporter(KIAA1382; SLC38A2). These transporters can facilitate the influx ofsubstrates into skeletal muscle, providing opportunities for muscletargeting.

In some embodiments, the muscle-targeting agent is a substrate of anequilibrative nucleoside transporter 2 (ENT2) transporter. Relative toother transporters, ENT2 has one of the highest mRNA expressions inskeletal muscle. While human ENT2 (hENT2) is expressed in most bodyorgans such as brain, heart, placenta, thymus, pancreas, prostate, andkidney, it is especially abundant in skeletal muscle. Human ENT2facilitates the uptake of its substrates depending on theirconcentration gradient. ENT2 plays a role in maintaining nucleosidehomeostasis by transporting a wide range of purine and pyrimidinenucleobases. The hENT2 transporter has a low affinity for allnucleosides (adenosine, guanosine, uridine, thymidine, and cytidine)except for inosine. Accordingly, in some embodiments, themuscle-targeting agent is an ENT2 substrate. Exemplary ENT2 substratesinclude, without limitation, inosine, 2′,3′-dideoxyinosine, andcalofarabine. In some embodiments, any of the muscle-targeting agentsprovided herein are associated with a molecular payload (e.g.,oligonucleotide payload). In some embodiments, the muscle-targetingagent is covalently linked to the molecular payload. In someembodiments, the muscle-targeting agent is non-covalently linked to themolecular payload.

In some embodiments, the muscle-targeting agent is a substrate of anorganic cation/carnitine transporter (OCTN2), which is a sodiumion-dependent, high affinity carnitine transporter. In some embodiments,the muscle-targeting agent is carnitine, mildronate, acetylcarnitine, orany derivative thereof that binds to OCTN2. In some embodiments, thecarnitine, mildronate, acetylcarnitine, or derivative thereof iscovalently linked to the molecular payload (e.g., oligonucleotidepayload).

A muscle-targeting agent may be a protein that is protein that exists inat least one soluble form that targets muscle cells. In someembodiments, a muscle-targeting protein may be hemojuvelin (also knownas repulsive guidance molecule C or hemochromatosis type 2 protein), aprotein involved in iron overload and homeostasis. In some embodiments,hemojuvelin may be full length or a fragment, or a mutant with at least75%, at least 80%, at least 85%, at least 90%, at least 95%, at least98% or at least 99% sequence identity to a functional hemojuvelinprotein. In some embodiments, a hemojuvelin mutant may be a solublefragment, may lack a N-terminal signaling, and/or lack a C-terminalanchoring domain. In some embodiments, hemojuvelin may be annotatedunder GenBank RefSeq Accession Numbers NM_001316767.1, NM_145277.4,NM_202004.3, NM_213652.3, or NM_213653.3. It should be appreciated thata hemojuvelin may be of human, non-human primate, or rodent origin.

B. Molecular Payloads

Some aspects of the disclosure provide molecular payloads, e.g., formodulating a biological outcome, e.g., the transcription of a DNAsequence, the expression of a protein, or the activity of a protein. Insome embodiments, a molecular payload is linked to, or otherwiseassociated with a muscle-targeting agent. In some embodiments, suchmolecular payloads are capable of targeting to a muscle cell, e.g., viaspecifically binding to a nucleic acid or protein in the muscle cellfollowing delivery to the muscle cell by an associated muscle-targetingagent. It should be appreciated that various types of muscle-targetingagents may be used in accordance with the disclosure. For example, themolecular payload may comprise, or consist of, an oligonucleotide (e.g.,antisense oligonucleotide), a peptide (e.g., a peptide that binds anucleic acid or protein associated with disease in a muscle cell), aprotein (e.g., a protein that binds a nucleic acid or protein associatedwith disease in a muscle cell), or a small molecule (e.g., a smallmolecule that modulates the function of a nucleic acid or proteinassociated with disease in a muscle cell). In some embodiments, themolecular payload is an oligonucleotide that comprises a strand having aregion of complementarity to a DUX4. Exemplary molecular payloads aredescribed in further detail herein, however, it should be appreciatedthat the exemplary molecular payloads provided herein are not meant tobe limiting.

i. Oligonucleotides

Any suitable oligonucleotide may be used as a molecular payload, asdescribed herein. In some embodiments, the oligonucleotide may bedesigned to cause degradation of an mRNA (e.g., the oligonucleotide maybe a gapmer, an siRNA, a ribozyme or an aptamer that causesdegradation). In some embodiments, the oligonucleotide may be designedto block translation of an mRNA (e.g., the oligonucleotide may be amixmer, an siRNA or an aptamer that blocks translation). In someembodiments, an oligonucleotide may be designed to cause degradation andblock translation of an mRNA. In some embodiments, an oligonucleotidemay be a guide nucleic acid (e.g., guide RNA) for directing activity ofan enzyme (e.g., a gene editing enzyme). Other examples ofoligonucleotides are provided herein. It should be appreciated that, insome embodiments, oligonucleotides in one format (e.g., antisenseoligonucleotides) may be suitably adapted to another format (e.g., siRNAoligonucleotides) by incorporating functional sequences (e.g., antisensestrand sequences) from one format to the other format.

Any suitable oligonucleotide may be used as a molecular payload, asdescribed herein. Examples of oligonucleotides useful for targeting DUX4are provided in U.S. Pat. No. 9,988,628, published on Feb. 2, 2017,entitled “AGENTS USEFUL IN TREATING FACIOSCAPULOHUMERAL MUSCULARDYSTROPHY”; U.S. Pat. No. 9,469,851, published Oct. 30, 2014, entitled“RECOMBINANT VIRUS PRODUCTS AND METHODS FOR INHIBITING EXPRESSION OFDUX4”; US Patent Application Publication 20120225034, published on Sep.6, 2012, entitled “AGENTS USEFUL IN TREATING FACIOSCAPULOHUMERALMUSCULAR DYSTROPHY”; PCT Patent Application Publication Number WO2013/120038, published on Aug. 15, 2013, entitled “MORPHOLINO TARGETINGDUX4 FOR TREATING FSHD”; Chen et al., “Morpholino-mediated Knockdown ofDUX4 Toward Facioscapulohumeral Muscular Dystrophy Therapeutics,”Molecular Therapy, 2016, 24:8, 1405-1411.; and Ansseau et al.,“Antisense Oligonucleotides Used to Target the DUX4 mRNA as TherapeuticApproaches in Facioscapulohumeral Muscular Dystrophy (FSHD),” Genes,2017, 8, 93; the contents of each of which are incorporated herein intheir entireties. In some embodiments, the oligonucleotide is anantisense oligonucleotide, a morpholino, a siRNA, a shRNA, or anothernucleotide which hybridizes with the target DUX4 gene or mRNA.

In some embodiments, oligonucleotides may have a region ofcomplementarity to a sequence as set forth as: Human DUX4, correspondingto NCBI sequence NM_001293798.1 (SEQ ID NO: 15) as below and/or MouseDUX4, corresponding to NCBI sequence NM_001081954.1 (SEQ ID NO: 16), asbelow. In some embodiments, the oligonucleotide may have a region ofcomplementarity to a hypomethylated, contracted D4Z4 repeat, as inDaxinger, et al., “Genetic and Epigenetic Contributors to FSHD,”published in Curr Opin Genet Dev in 2015, Lim J-W, et al.,DICER/AGO-dependent epigenetic silencing of D4Z4 repeats enhanced byexogenous siRNA suggests mechanisms and therapies for FSHD Hum MolGenet. 2015 Sep. 1; 24(17): 4817-4828, the contents of each of which areincorporated in their entireties.

In some embodiments, oligonucleotides may have a region ofcomplementarity to a sequence set forth as follows, which is an examplehuman DUX4 gene sequence (NM_001293798.1) (SEQ ID NO: 15):

ATGGCCCTCCCGACACCCTCGGACAGCACCCTCCCCGCGGAAGCCCGGGGACGAGGACGGCGACGGAGACTCGTTTGGACCCCGAGCCAAAGCGAGGCCCTGCGAGCCTGCTTTGAGCGGAACCCGTACCCGGGCATCGCCACCAGAGAACGGCTGGCCCAGGCCATCGGCATTCCGGAGCCCAGGGTCCAGATTTGGTTTCAGAATGAGAGGTCACGCCAGCTGAGGCAGCACCGGCGGGAATCTCGGCCCTGGCCCGGGAGACGCGGCCCGCCAGAAGGCCGGCGAAAGCGGACCGCCGTCACCGGATCCCAGACCGCCCTGCTCCTCCGAGCCTTTGAGAAGGATCGCTTTCCAGGCATCGCCGCCCGGGAGGAGCTGGCCAGAGAGACGGGCCTCCCGGAGTCCAGGATTCAGATCTGGTTTCAGAATCGAAGGGCCAGGCACCCGGGACAGGGTGGCAGGGCGCCCGCGCAGGCAGGCGGCCTGTGCAGCGCGGCCCCCGGCGGGGGTCACCCTGCTCCCTCGTGGGTCGCCTTCGCCCACACCGGCGCGTGGGGAACGGGGCTTCCCGCACCCCACGTGCCCTGCGCGCCTGGGGCTCTCCCACAGGGGGCTTTCGTGAGCCAGGCAGCGAGGGCCGCCCCCGCGCTGCAGCCCAGCCAGGCCGCGCCGGCAGAGGGGATCTCCCAACCTGCCCCGGCGCGCGGGGATTTCGCCTACGCCGCCCCGGCTCCTCCGGACGGGGCGCTCTCCCACCCTCAGGCTCCTCGGTGGCCTCCGCACCCGGGCAAAAGCCGGGAGGACCGGGACCCGCAGCGCGACGGCCTGCCGGGCCCCTGCGCGGTGGCACAGCCTGGGCCCGCTCAAGCGGGGCCGCAGGGCCAAGGGGTGCTTGCGCCACCCACGTCCCAGGGGAGTCCGTGGTGGGGCTGGGGCCGGGGTCCCCAGGTCGCCGGGGCGGCGTGGGAACCCCAAGCCGGGGCAGCTCCACCTCCCCAGCCCGCGCCCCCGGACGCCTCCGCCTCCGCGCGGCAGGGGCAGATGCAAGGCATCCCGGCGCCCTCCCAGGCGCTCCAGGAGCCGGCGCCCTGGTCTGCACTCCCCTGCGGCCTGCTGCTGGATGAGCTCCTGGCGAGCCCGGAGTTTCTGCAGCAGGCGCAACCTCTCCTAGAAACGGAGGCCCCGGGGGAGCTGGAGGCCTCGGAAGAGGCCGCCTCGCTGGAAGCACCCCTCAGCGAGGAAGAATACCGGGCTCTGCTGGAGGAGCTTTAG

In some embodiments, oligonucleotides may have a region ofcomplementarity to a sequence set forth as follows, which is an examplemouse DUX4 gene sequence (SEQ ID NO: 16) (NM_001081954.1):

ATGGCAGAAGCTGGCAGCCCTGTTGGTGGCAGTGGTGTGGCACGGGAATCCCGGCGGCGCAGGAAGACGGTTTGGCAGGCCTGGCAAGAGCAGGCCCTGCTATCAACTTTCAAGAAGAAGAGATACCTGAGCTTCAAGGAGAGGAAGGAGCTGGCCAAGCGAATGGGGGTCTCAGATTGCCGCATCCGCGTGTGGTTTCAGAACCGCAGGAATCGCAGTGGAGAGGAGGGGCATGCCTCAAAGAGGTCCATCAGAGGCTCCAGGCGGCTAGCCTCGCCACAGCTCCAGGAAGAGCTTGGATCCAGGCCACAGGGTAGAGGCATGCGCTCATCTGGCAGAAGGCCTCGCACTCGACTCACCTCGCTACAGCTCAGGATCCTAGGGCAAGCCTTTGAGAGGAACCCACGACCAGGCTTTGCTACCAGGGAGGAGCTGGCGCGTGACACAGGGTTGCCCGAGGACACGATCCACATATGGTTTCAAAACCGAAGAGCTCGGCGGCGCCACAGGAGGGGCAGGCCCACAGCTCAAGATCAAGACTTGCTGGCGTCACAAGGGTCGGATGGGGCCCCTGCAGGTCCGGAAGGCAGAGAGCGTGAAGGTGCCCAGGAGAACTTGTTGCCACAGGAAGAAGCAGGAAGTACGGGCATGGATACCTCGAGCCCTAGCGACTTGCCCTCCTTCTGCGGAGAGTCCCAGCCTTTCCAAGTGGCACAGCCCCGTGGAGCAGGCCAACAAGAGGCCCCCACTCGAGCAGGCAACGCAGGCTCTCTGGAACCCCTCCTTGATCAGCTGCTGGATGAAGTCCAAGTAGAAGAGCCTGCTCCAGCCCCTCTGAATTTGGATGGAGACCCTGGTGGCAGGGTGCATGAAGGTTCCCAGGAGAGCTTTTGGCCACAGGAAGAAGCAGGAAGTACAGGCATGGATACTTCTAGCCCCAGCGACTCAAACTCCTTCTGCAGAGAGTCCCAGCCTTCCCAAGTGGCACAGCCCTGTGGAGCGGGCCAAGAAGATGCCCGCACTCAAGCAGACAGCACAGGCCCTCTGGAACTCCTCCTCCTTGATCAACTGCTGGACGAAGTCCAAAAGGAAGAGCATGTGCCAGTCCCACTGGATTGGGGTAGAAATCCTGGCAGCAGGGAGCATGAAGGTTCCCAGGACAGCTTACTGCCCCTGGAGGAAGCAGTAAATTCGGGCATGGATACCTCGATCCCTAGCATCTGGCCAACCTTCTGCAGAGAATCCCAGCCTCCCCAAGTGGCACAGCCCTCTGGACCAGGCCAAGCACAGGCCCCCACTCAAGGTGGGAACACGGACCCCCTGGAGCTCTTCCTCTATCAACTGTTGGATGAAGTCCAAGTAGAAGAGCATGCTCCAGCCCCTCTGAATTGGGATGTAGATCCTGGTGGCAGGGTGCATGAAGGTTCGTGGGAGAGCTTTTGGCCACAGGAAGAAGCAGGAAGTACAGGCCTGGATACTTCAAGCCCCAGCGACTCAAACTCCTTCTTCAGAGAGTCCAAGCCTTCCCAAGTGGCACAGCGCCGTGGAGCGGGCCAAGAAGATGCCCGCACTCAAGCAGACAGCACAGGCCCTCTGGAACTCCTCCTCTTTGATCAACTGCTGGACGAAGTCCAAAAGGAAGAGCATGTGCCAGCCCCACTGGATTGGGGTAGAAATCCTGGCAGCATGGAGCATGAAGGTTCCCAGGACAGCTTACTGCCCCTGGAGGAAGCAGCAAATTCGGGCAGGGATACCTCGATCCCTAGCATCTGGCCAGCCTTCTGCAGAAAATCCCAGCCTCCCCAAGTGGCACAGCCCTCTGGACCAGGCCAAGCACAGGCCCCCATTCAAGGTGGGAACACGGACCCCCTGGAGCTCTTCCTTGATCAACTGCTGACCGAAGTCCAACTTGAGGAGCAGGGGCCTGCCCCTGTGAATGTGGAGGAAACATGGGAGCAAATGGACACAACACCTATCTGCCTCTCACTTCAGAAGAATATCAGACTCTTCTAGATATGCTCTGA.

In some embodiments, an oligonucleotide may have a region ofcomplementarity to DUX4 gene sequences of multiple species, e.g.,selected from human, mouse and non-human species.

In some embodiments, an oligonucleotide that targets DUX4 is a FM10sequence. In some embodiments, an oligonucleotide that targets DUX4 is aphosphorodiamidate morpholino version of a FM10 sequence. In someembodiments, an oligonucleotide that targets DUX4 comprises the sequenceGGGCATTTTAATATATCTCTGAACT (SEQ ID NO: 45). In some embodiments, anoligonucleotide that targets DUX4 comprises a sequence that iscomplementary to at least 15 consecutive nucleotides of

(SEQ ID NO: 46) AGTTCAGAGATATATTAAAATGCCC.

In some embodiments, muscle specific E3 ubiquitin ligases areoverexpressed in FSHD and function in muscle atrophy (see, e.g.,Vanderplanck, C. et al. “The FSHD Atrophic Myotube Phenotype Is Causedby DUX4 Expression” PLoS One 6,10:e26820, 2011). In some embodiments,downregulation of these ligases presents a viable therapeutic strategy.In some embodiments, an oligonucleotide may target, e.g., inhibit theexpression of, a muscle specific E3 ubiquitin ligase implicated in FSHD,such as MuRF1 (also known as TRIM63) and MAFbx (also known as Fbx032).In some embodiments, an oligonucleotide may have a region ofcomplementarity to at least one MuRF1 gene sequence, e.g. human MuRF1(NCBI Gene ID 84676). In some embodiments, an oligonucleotide may have aregion of complementarity to at least one MAFbx gene sequence, e.g.human MAFbx (NCBI Gene ID 114907).

a. Oligonucleotide Size/Sequence

Oligonucleotides may be of a variety of different lengths, e.g.,depending on the format. In some embodiments, an oligonucleotide is 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, 30, 35, 40, 45, 50, 75, or more nucleotides in length.In a some embodiments, the oligonucleotide is 8 to 50 nucleotides inlength, 8 to 40 nucleotides in length, 8 to 30 nucleotides in length, 10to 15 nucleotides in length, 10 to 20 nucleotides in length, 15 to 25nucleotides in length, 21 to 23 nucleotides in lengths, etc.

In some embodiments, a complementary nucleic acid sequence of anoligonucleotide for purposes of the present disclosure is specificallyhybridizable or specific for the target nucleic acid when binding of thesequence to the target molecule (e.g., mRNA) interferes with the normalfunction of the target (e.g., mRNA) to cause a loss of activity (e.g.,inhibiting translation) or expression (e.g., degrading a target mRNA)and there is a sufficient degree of complementarity to avoidnon-specific binding of the sequence to non-target sequences underconditions in which avoidance of non-specific binding is desired, e.g.,under physiological conditions in the case of in vivo assays ortherapeutic treatment, and in the case of in vitro assays, underconditions in which the assays are performed under suitable conditionsof stringency. Thus, in some embodiments, an oligonucleotide may be atleast 80%, at least 85%, at least 90%, at least 91%, at least 92%, atleast 93%, at least 94%, at least 95%, at least 96%, at least 97%, atleast 98%, at least 99% or 100% complementary to the consecutivenucleotides of an target nucleic acid. In some embodiments acomplementary nucleotide sequence need not be 100% complementary to thatof its target to be specifically hybridizable or specific for a targetnucleic acid.

In some embodiments, an oligonucleotide comprises region ofcomplementarity to a target nucleic acid that is in the range of 8 to15, 8 to 30, 8 to 40, or 10 to 50, or 5 to 50, or 5 to 40 nucleotides inlength. In some embodiments, a region of complementarity of anoligonucleotide to a target nucleic acid is 5, 6, 7, 8, 9, 10, 11, 12,13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30,31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48,49, or 50 nucleotides in length. In some embodiments, the region ofcomplementarity is complementary with at least 8 consecutive nucleotidesof a target nucleic acid. In some embodiments, an oligonucleotide maycontain 1, 2 or 3 base mismatches compared to the portion of theconsecutive nucleotides of target nucleic acid. In some embodiments theoligonucleotide may have up to 3 mismatches over 15 bases, or up to 2mismatches over 10 bases.

b. Oligonucleotide Modifications:

The oligonucleotides described herein may be modified, e.g., comprise amodified sugar moiety, a modified internucleoside linkage, a modifiednucleotide and/or combinations thereof. In addition, in someembodiments, oligonucleotides may exhibit one or more of the followingproperties: do not mediate alternative splicing; are not immunestimulatory; are nuclease resistant; have improved cell uptake comparedto unmodified oligonucleotides; are not toxic to cells or mammals; haveimproved endosomal exit internally in a cell; minimizes TLR stimulation;or avoid pattern recognition receptors. Any of the modified chemistriesor formats of oligonucleotides described herein can be combined witheach other. For example, one, two, three, four, five, or more differenttypes of modifications can be included within the same oligonucleotide.

In some embodiments, certain nucleotide modifications may be used thatmake an oligonucleotide into which they are incorporated more resistantto nuclease digestion than the native oligodeoxynucleotide oroligoribonucleotide molecules; these modified oligonucleotides surviveintact for a longer time than unmodified oligonucleotides. Specificexamples of modified oligonucleotides include those comprising modifiedbackbones, for example, modified internucleoside linkages such asphosphorothioates, phosphotriesters, methyl phosphonates, short chainalkyl or cycloalkyl intersugar linkages or short chain heteroatomic orheterocyclic intersugar linkages. Accordingly, oligonucleotides of thedisclosure can be stabilized against nucleolytic degradation such as bythe incorporation of a modification, e.g., a nucleotide modification.

In some embodiments, an oligonucleotide may be of up to 50 or up to 100nucleotides in length in which 2 to 10, 2 to 15, 2 to 16, 2 to 17, 2 to18, 2 to 19, 2 to 20, 2 to 25, 2 to 30, 2 to 40, 2 to 45, or morenucleotides of the oligonucleotide are modified nucleotides. Theoligonucleotide may be of 8 to 30 nucleotides in length in which 2 to10, 2 to 15, 2 to 16, 2 to 17, 2 to 18, 2 to 19, 2 to 20, 2 to 25, 2 to30 nucleotides of the oligonucleotide are modified nucleotides. Theoligonucleotide may be of 8 to 15 nucleotides in length in which 2 to 4,2 to 5, 2 to 6, 2 to 7, 2 to 8, 2 to 9, 2 to 10, 2 to 11, 2 to 12, 2 to13, 2 to 14 nucleotides of the oligonucleotide are modified nucleotides.Optionally, the oligonucleotides may have every nucleotide except 1, 2,3, 4, 5, 6, 7, 8, 9, or 10 nucleotides modified. Oligonucleotidemodifications are described further herein.

c. Modified Nucleotides

In some embodiments, an oligonucleotide include a 2′-modifiednucleotide, e.g., a 2′-deoxy, 2′-deoxy-2′-fluoro, 2′-O-methyl,2′-O-methoxyethyl (2′-O-MOE), 2′-O-aminopropyl (2′-O-AP),2′-O-dimethylaminoethyl (2′-O-DMAOE), 2′-O-dimethylaminopropyl(2′-O-DMAP), 2′-O-dimethylaminoethyloxyethyl (2′-O-DMAEOE), or2′-O—N-methylacetamido (2′-O-NMA).

In some embodiments, an oligonucleotide can include at least one2′-O-methyl-modified nucleotide, and in some embodiments, all of thenucleotides include a 2′-O-methyl modification. In some embodiments, anoligonucleotide comprises modified nucleotides in which the ribose ringcomprises a bridge moiety connecting two atoms in the ring, e.g.,connecting the 2′-0 atom to the 4′-C atom. In some embodiments, theoligonucleotides are “locked,” e.g., comprise modified nucleotides inwhich the ribose ring is “locked” by a methylene bridge connecting the2′-0 atom and the 4′-C atom. Examples of LNAs are described inInternational Patent Application Publication WO/2008/043753, publishedon Apr. 17, 2008, and entitled “RNA Antagonist Compounds For TheModulation Of PCSK9”, the contents of which are incorporated herein byreference in its entirety.

Other modifications that may be used in the oligonucleotides disclosedherein include ethylene-bridged nucleic acids (ENAs). ENAs include, butare not limited to, 2′-0,4′-C-ethylene-bridged nucleic acids. Examplesof ENAs are provided in International Patent Publication No. WO2005/042777, published on May 12, 2005, and entitled “APP/ENAAntisense”; Morita et al., Nucleic Acid Res., Suppl 1:241-242, 2001;Surono et al., Hum. Gene Ther., 15:749-757, 2004; Koizumi, Curr. Opin.Mol. Ther., 8:144-149, 2006 and Horie et al., Nucleic Acids Symp. Ser(Oxf), 49:171-172, 2005; the disclosures of which are incorporatedherein by reference in their entireties.

In some embodiments, the oligonucleotide may comprise a bridgednucleotide, such as a locked nucleic acid (LNA) nucleotide, aconstrained ethyl (cEt) nucleotide, or an ethylene bridged nucleic acid(ENA) nucleotide. In some embodiments, the oligonucleotide comprises amodified nucleotide disclosed in one of the following United Statespatent or patent application Publications: U.S. Pat. No. 7,399,845,issued on Jul. 15, 2008, and entitled “6-Modified Bicyclic Nucleic AcidAnalogs”; U.S. Pat. No. 7,741,457, issued on Jun. 22, 2010, and entitled“6-Modified Bicyclic Nucleic Acid Analogs”; U.S. Pat. No. 8,022,193,issued on Sep. 20, 2011, and entitled “6-Modified Bicyclic Nucleic AcidAnalogs”; U.S. Pat. No. 7,569,686, issued on Aug. 4, 2009, and entitled“Compounds And Methods For Synthesis Of Bicyclic Nucleic Acid Analogs”;U.S. Pat. No. 7,335,765, issued on Feb. 26, 2008, and entitled “NovelNucleoside And Oligonucleotide Analogues”; U.S. Pat. No. 7,314,923,issued on Jan. 1, 2008, and entitled “Novel Nucleoside AndOligonucleotide Analogues”; U.S. Pat. No. 7,816,333, issued on Oct. 19,2010, and entitled “Oligonucleotide Analogues And Methods Utilizing TheSame” and US Publication Number 2011/0009471 now U.S. Pat. No.8,957,201, issued on Feb. 17, 2015, and entitled “OligonucleotideAnalogues And Methods Utilizing The Same”, the entire contents of eachof which are incorporated herein by reference for all purposes.

In some embodiments, the oligonucleotide comprises at least onenucleotide modified at the 2′ position of the sugar, preferably a2′-O-alkyl, 2′-O-alkyl-O-alkyl or 2′-fluoro-modified nucleotide. Inother preferred embodiments, RNA modifications include 2′-fluoro,2′-amino and 2′ O-methyl modifications on the ribose of pyrimidines,abasic residues or an inverted base at the 3′ end of the RNA.

In some embodiments, the oligonucleotide may have at least one modifiednucleotide that results in an increase in Tm of the oligonucleotide in arange of 1° C., 2° C., 3° C., 4° C., or 5° C. compared with anoligonucleotide that does not have the at least one modified nucleotide.The oligonucleotide may have a plurality of modified nucleotides thatresult in a total increase in Tm of the oligonucleotide in a range of 2°C., 3° C., 4° C., 5° C., 6° C., 7° C., 8° C., 9° C., 10° C., 15° C., 20°C., 25° C., 30° C., 35° C., 40° C., 45° C. or more compared with anoligonucleotide that does not have the modified nucleotide.

The oligonucleotide may comprise alternating nucleotides of differentkinds. For example, an oligonucleotide may comprise alternatingdeoxyribonucleotides or ribonucleotides and2′-fluoro-deoxyribonucleotides. An oligonucleotide may comprisealternating deoxyribonucleotides or ribonucleotides and 2′-O-methylnucleotides. An oligonucleotide may comprise alternating 2′-fluoronucleotides and 2′-O-methyl nucleotides. An oligonucleotide may comprisealternating bridged nucleotides and 2′-fluoro or 2′-O-methylnucleotides.

d. Internucleotide Linkages/Backbones

In some embodiments, oligonucleotide may contain a phosphorothioate orother modified internucleotide linkage. In some embodiments, theoligonucleotide comprises phosphorothioate internucleoside linkages. Insome embodiments, the oligonucleotide comprises phosphorothioateinternucleoside linkages between at least two nucleotides. In someembodiments, the oligonucleotide comprises phosphorothioateinternucleoside linkages between all nucleotides. For example, in someembodiments, oligonucleotides comprise modified internucleotide linkagesat the first, second, and/or third internucleoside linkage at the 5′ or3′ end of the nucleotide sequence.

Phosphorus-containing linkages that may be used include, but are notlimited to, phosphorothioates, chiral phosphorothioates,phosphorodithioates, phosphotriesters, aminoalkylphosphotriesters,methyl and other alkyl phosphonates comprising 3′alkylene phosphonatesand chiral phosphonates, phosphinates, phosphoramidates comprising3′-amino phosphoramidate and aminoalkylphosphoramidates,thionophosphoramidates, thionoalkylphosphonates,thionoalkylphosphotriesters, and boranophosphates having normal 3′-5′linkages, 2′-5′ linked analogs of these, and those having invertedpolarity wherein the adjacent pairs of nucleoside units are linked 3′-5′to 5′-3′ or 2′-5′ to 5′-2′; see U.S. Pat. Nos. 3,687,808; 4,469,863;4,476,301; 5,023,243; 5,177,196; 5,188,897; 5,264,423; 5,276,019;5,278,302; 5,286,717; 5,321,131; 5,399,676; 5,405,939; 5,453,496; 5,455,233; 5,466,677; 5,476,925; 5,519,126; 5,536,821; 5,541,306; 5,550,111;5,563, 253; 5,571,799; 5,587,361; and 5,625,050.

In some embodiments, oligonucleotides may have heteroatom backbones,such as methylene(methylimino) or MMI backbones; amide backbones (see DeMesmaeker et al. Ace. Chem. Res. 1995, 28:366-374); morpholino backbones(see Summerton and Weller, U.S. Pat. No. 5,034,506); or peptide nucleicacid (PNA) backbones (wherein the phosphodiester backbone of theoligonucleotide is replaced with a polyamide backbone, the nucleotidesbeing bound directly or indirectly to the aza nitrogen atoms of thepolyamide backbone, see Nielsen et al., Science 1991, 254, 1497).

e. Stereospecific Oligonucleotides

In some embodiments, internucleotidic phosphorus atoms ofoligonucleotides are chiral, and the properties of the oligonucleotidesare adjusted based on the configuration of the chiral phosphorus atoms.In some embodiments, appropriate methods may be used to synthesizeP-chiral oligonucleotide analogs in a stereocontrolled manner (e.g., asdescribed in Oka N, Wada T, Stereocontrolled synthesis ofoligonucleotide analogs containing chiral internucleotidic phosphorusatoms. Chem Soc Rev. 2011 December; 40(12):5829-43.) In someembodiments, phosphorothioate containing oligonucleotides are providedthat comprise nucleoside units that are joined together by eithersubstantially all Sp or substantially all Rp phosphorothioate intersugarlinkages. In some embodiments, such phosphorothioate oligonucleotideshaving substantially chirally pure intersugar linkages are prepared byenzymatic or chemical synthesis, as described, for example, in U.S. Pat.No. 5,587,261, issued on Dec. 12, 1996, the contents of which areincorporated herein by reference in their entirety. In some embodiments,chirally controlled oligonucleotides provide selective cleavage patternsof a target nucleic acid. For example, in some embodiments, a chirallycontrolled oligonucleotide provides single site cleavage within acomplementary sequence of a nucleic acid, as described, for example, inUS Patent Application Publication 20170037399 A1, published on Feb. 2,2017, entitled “CHIRAL DESIGN”, the contents of which are incorporatedherein by reference in their entirety.

f. Morpholinos

In some embodiments, the oligonucleotide may be a morpholino-basedcompounds. Morpholino-based oligomeric compounds are described in DwaineA. Braasch and David R. Corey, Biochemistry, 2002, 41(14), 4503-4510);Genesis, volume 30, issue 3, 2001; Heasman, J., Dev. Biol., 2002, 243,209-214; Nasevicius et al., Nat. Genet., 2000, 26, 216-220; Lacerra etal., Proc. Natl. Acad. Sci., 2000, 97, 9591-9596; and U.S. Pat. No.5,034,506, issued Jul. 23, 1991. In some embodiments, themorpholino-based oligomeric compound is a phosphorodiamidate morpholinooligomer (PMO) (e.g., as described in Iverson, Curr. Opin. Mol. Ther.,3:235-238, 2001; and Wang et al., J. Gene Med., 12:354-364, 2010; thedisclosures of which are incorporated herein by reference in theirentireties).

g. Peptide Nucleic Acids (PNAs)

In some embodiments, both a sugar and an internucleoside linkage (thebackbone) of the nucleotide units of an oligonucleotide are replacedwith novel groups. In some embodiments, the base units are maintainedfor hybridization with an appropriate nucleic acid target compound. Onesuch oligomeric compound, an oligonucleotide mimetic that has been shownto have excellent hybridization properties, is referred to as a peptidenucleic acid (PNA). In PNA compounds, the sugar-backbone of anoligonucleotide is replaced with an amide containing backbone, forexample, an aminoethylglycine backbone. The nucleobases are retained andare bound directly or indirectly to aza nitrogen atoms of the amideportion of the backbone. Representative publication that report thepreparation of PNA compounds include, but are not limited to, U.S. Pat.Nos. 5,539,082; 5,714,331; and 5,719,262, each of which is hereinincorporated by reference. Further teaching of PNA compounds can befound in Nielsen et al., Science, 1991, 254, 1497-1500.

h. Gapmers

In some embodiments, the oligonucleotide is a gapmer. A gapmeroligonucleotide generally has the formula 5′-X-Y-Z-3′, with X and Z asflanking regions around a gap region Y. In some embodiments, the Yregion is a contiguous stretch of nucleotides, e.g., a region of atleast 6 DNA nucleotides, which are capable of recruiting an RNAse, suchas RNAse H. In some embodiments, the gapmer binds to the target nucleicacid, at which point an RNAse is recruited and can then cleave thetarget nucleic acid. In some embodiments, the Y region is flanked both5′ and 3′ by regions X and Z comprising high-affinity modifiednucleotides, e.g., one to six modified nucleotides. Examples of modifiednucleotides include, but are not limited to, 2′ MOE or 2′OMe or LockedNucleic Acid bases (LNA). The flanking sequences X and Z may be of oneto twenty nucleotides, one to eight nucleotides or one to fivenucleotides in length, in some embodiments. The flanking sequences X andZ may be of similar length or of dissimilar lengths. The gap-segment Ymay be a nucleotide sequence of five to twenty nucleotides, size totwelve nucleotides or six to ten nucleotides in length, in someembodiments.

In some embodiments, the gap region of the gapmer oligonucleotides maycontain modified nucleotides known to be acceptable for efficient RNaseH action in addition to DNA nucleotides, such as C4′-substitutednucleotides, acyclic nucleotides, and arabino-configured nucleotides. Insome embodiments, the gap region comprises one or more unmodifiedinternucleosides. In some embodiments, one or both flanking regions eachindependently comprise one or more phosphorothioate internucleosidelinkages (e.g., phosphorothioate internucleoside linkages or otherlinkages) between at least two, at least three, at least four, at leastfive or more nucleotides. In some embodiments, the gap region and twoflanking regions each independently comprise modified internucleosidelinkages (e.g., phosphorothioate internucleoside linkages or otherlinkages) between at least two, at least three, at least four, at leastfive or more nucleotides.

A gapmer may be produced using appropriate methods. Representative U.S.patents, U.S. patent publications, and PCT publications that teach thepreparation of gapmers include, but are not limited to, U.S. Pat. Nos.5,013,830; 5,149,797; 5,220,007; 5,256,775; 5,366,878; 5,403,711;5,491,133; 5,565,350; 5,623,065; 5,652,355; 5,652,356; 5,700,922;5,898,031; 7,432,250; and 7,683,036; U.S. patent publication Nos.US20090286969, US20100197762, and US20110112170; and PCT publicationNos. WO2008049085 and WO2009090182, each of which is herein incorporatedby reference in its entirety.

i. Mixmers

In some embodiments, an oligonucleotide described herein may be a mixmeror comprise a mixmer sequence pattern. In general, mixmers areoligonucleotides that comprise both naturally and non-naturallyoccurring nucleotides or comprise two different types of non-naturallyoccurring nucleotides typically in an alternating pattern. Mixmersgenerally have higher binding affinity than unmodified oligonucleotidesand may be used to specifically bind a target molecule, e.g., to block abinding site on the target molecule. Generally, mixmers do not recruitan RNAse to the target molecule and thus do not promote cleavage of thetarget molecule. Such oligonucleotides that are incapable of recruitingRNAse H have been described, for example, see WO2007/112754 orWO2007/112753.

In some embodiments, the mixmer comprises or consists of a repeatingpattern of nucleotide analogues and naturally occurring nucleotides, orone type of nucleotide analogue and a second type of nucleotideanalogue. However, a mixmer need not comprise a repeating pattern andmay instead comprise any arrangement of modified nucleotides andnaturally occurring nucleotides or any arrangement of one type ofmodified nucleotide and a second type of modified nucleotide. Therepeating pattern, may, for instance be every second or every thirdnucleotide is a modified nucleotide, such as LNA, and the remainingnucleotides are naturally occurring nucleotides, such as DNA, or are a2′ substituted nucleotide analogue such as 2′MOE or 2′ fluoro analogues,or any other modified nucleotide described herein. It is recognized thatthe repeating pattern of modified nucleotide, such as LNA units, may becombined with modified nucleotide at fixed positions—e.g. at the 5′ or3′ termini.

In some embodiments, a mixmer does not comprise a region of more than 5,more than 4, more than 3, or more than 2 consecutive naturally occurringnucleotides, such as DNA nucleotides. In some embodiments, the mixmercomprises at least a region consisting of at least two consecutivemodified nucleotide, such as at least two consecutive LNAs. In someembodiments, the mixmer comprises at least a region consisting of atleast three consecutive modified nucleotide units, such as at leastthree consecutive LNAs.

In some embodiments, the mixmer does not comprise a region of more than7, more than 6, more than 5, more than 4, more than 3, or more than 2consecutive nucleotide analogues, such as LNAs. In some embodiments, LNAunits may be replaced with other nucleotide analogues, such as thosereferred to herein.

Mixmers may be designed to comprise a mixture of affinity enhancingmodified nucleotides, such as in non-limiting example LNA nucleotidesand 2′-O-methyl nucleotides. In some embodiments, a mixmer comprisesmodified internucleoside linkages (e.g., phosphorothioateinternucleoside linkages or other linkages) between at least two, atleast three, at least four, at least five or more nucleotides.

A mixmer may be produced using any suitable method. Representative U.S.patents, U.S. patent publications, and PCT publications that teach thepreparation of mixmers include U.S. patent publication Nos.US20060128646, US20090209748, US20090298916, US20110077288, andUS20120322851, and U.S. Pat. No. 7,687,617.

In some embodiments, a mixmer comprises one or more morpholinonucleotides. For example, in some embodiments, a mixmer may comprisemorpholino nucleotides mixed (e.g., in an alternating manner) with oneor more other nucleotides (e.g., DNA, RNA nucleotides) or modifiednucleotides (e.g., LNA, 2′-O-Methyl nucleotides).

In some embodiments, mixmers are useful for splice correcting or exonskipping, for example, as reported in Touznik A., et al., LNA/DNAmixmer-based antisense oligonucleotides correct alternative splicing ofthe SMN2 gene and restore SMN protein expression in type 1 SMAfibroblasts Scientific Reports, volume 7, Article number: 3672 (2017),Chen S. et al., Synthesis of a Morpholino Nucleic Acid (MNA)-UridinePhosphoramidite, and Exon Skipping Using MNA/2′-O-Methyl MixmerAntisense Oligonucleotide, Molecules 2016, 21, 1582, the contents ofeach which are incorporated herein by reference.

j. RNA Interference (RNAi)

In some embodiments, oligonucleotides provided herein may be in the formof small interfering RNAs (siRNA), also known as short interfering RNAor silencing RNA. SiRNA, is a class of double-stranded RNA molecules,typically about 20-25 base pairs in length that target nucleic acids(e.g., mRNAs) for degradation via the RNA interference (RNAi) pathway incells. Specificity of siRNA molecules may be determined by the bindingof the antisense strand of the molecule to its target RNA. EffectivesiRNA molecules are generally less than 30 to 35 base pairs in length toprevent the triggering of non-specific RNA interference pathways in thecell via the interferon response, although longer siRNA can also beeffective.

Following selection of an appropriate target RNA sequence, siRNAmolecules that comprise a nucleotide sequence complementary to all or aportion of the target sequence, i.e. an antisense sequence, can bedesigned and prepared using appropriate methods (see, e.g., PCTPublication Number WO 2004/016735; and U.S. Patent Publication Nos.2004/0077574 and 2008/0081791).

The siRNA molecule can be double stranded (i.e. a dsRNA moleculecomprising an antisense strand and a complementary sense strand) orsingle-stranded (i.e. a ssRNA molecule comprising just an antisensestrand). The siRNA molecules can comprise a duplex, asymmetric duplex,hairpin or asymmetric hairpin secondary structure, havingself-complementary sense and antisense strands.

Double-stranded siRNA may comprise RNA strands that are the same lengthor different lengths. Double-stranded siRNA molecules can also beassembled from a single oligonucleotide in a stem-loop structure,wherein self-complementary sense and antisense regions of the siRNAmolecule are linked by means of a nucleic acid based or non-nucleicacid-based linker(s), as well as circular single-stranded RNA having twoor more loop structures and a stem comprising self-complementary senseand antisense strands, wherein the circular RNA can be processed eitherin vivo or in vitro to generate an active siRNA molecule capable ofmediating RNAi. Small hairpin RNA (shRNA) molecules thus are alsocontemplated herein. These molecules comprise a specific antisensesequence in addition to the reverse complement (sense) sequence,typically separated by a spacer or loop sequence. Cleavage of the spaceror loop provides a single-stranded RNA molecule and its reversecomplement, such that they may anneal to form a dsRNA molecule(optionally with additional processing steps that may result in additionor removal of one, two, three or more nucleotides from the 3′ end and/orthe 5′ end of either or both strands). A spacer can be of a sufficientlength to permit the antisense and sense sequences to anneal and form adouble-stranded structure (or stem) prior to cleavage of the spacer(and, optionally, subsequent processing steps that may result inaddition or removal of one, two, three, four, or more nucleotides fromthe 3′ end and/or the 5′ end of either or both strands). A spacersequence is may be an unrelated nucleotide sequence that is situatedbetween two complementary nucleotide sequence regions which, whenannealed into a double-stranded nucleic acid, comprise a shRNA.

The overall length of the siRNA molecules can vary from about 14 toabout 100 nucleotides depending on the type of siRNA molecule beingdesigned. Generally between about 14 and about 50 of these nucleotidesare complementary to the RNA target sequence, i.e. constitute thespecific antisense sequence of the siRNA molecule. For example, when thesiRNA is a double- or single-stranded siRNA, the length can vary fromabout 14 to about 50 nucleotides, whereas when the siRNA is a shRNA orcircular molecule, the length can vary from about 40 nucleotides toabout 100 nucleotides.

An siRNA molecule may comprise a 3′ overhang at one end of the molecule,The other end may be blunt-ended or have also an overhang (5′ or 3′).When the siRNA molecule comprises an overhang at both ends of themolecule, the length of the overhangs may be the same or different. Inone embodiment, the siRNA molecule of the present disclosure comprises3′ overhangs of about 1 to about 3 nucleotides on both ends of themolecule.

k. microRNA (miRNAs)

In some embodiments, an oligonucleotide may be a microRNA (miRNA).MicroRNAs (referred to as “miRNAs”) are small non-coding RNAs, belongingto a class of regulatory molecules that control gene expression bybinding to complementary sites on a target RNA transcript. Typically,miRNAs are generated from large RNA precursors (termed pri-miRNAs) thatare processed in the nucleus into approximately 70 nucleotidepre-miRNAs, which fold into imperfect stem-loop structures. Thesepre-miRNAs typically undergo an additional processing step within thecytoplasm where mature miRNAs of 18-25 nucleotides in length are excisedfrom one side of the pre-miRNA hairpin by an RNase III enzyme, Dicer.

As used herein, miRNAs including pri-miRNA, pre-miRNA, mature miRNA orfragments of variants thereof that retain the biological activity ofmature miRNA. In one embodiment, the size range of the miRNA can be from21 nucleotides to 170 nucleotides. In one embodiment the size range ofthe miRNA is from 70 to 170 nucleotides in length. In anotherembodiment, mature miRNAs of from 21 to 25 nucleotides in length can beused.

l. Aptamers

In some embodiments, oligonucleotides provided herein may be in the formof aptamers. Generally, in the context of molecular payloads, aptamer isany nucleic acid that binds specifically to a target, such as a smallmolecule, protein, nucleic acid in a cell. In some embodiments, theaptamer is a DNA aptamer or an RNA aptamer. In some embodiments, anucleic acid aptamer is a single-stranded DNA or RNA (ssDNA or ssRNA).It is to be understood that a single-stranded nucleic acid aptamer mayform helices and/or loop structures. The nucleic acid that forms thenucleic acid aptamer may comprise naturally occurring nucleotides,modified nucleotides, naturally occurring nucleotides with hydrocarbonlinkers (e.g., an alkylene) or a polyether linker (e.g., a PEG linker)inserted between one or more nucleotides, modified nucleotides withhydrocarbon or PEG linkers inserted between one or more nucleotides, ora combination of thereof. Exemplary publications and patents describingaptamers and method of producing aptamers include, e.g., Lorsch andSzostak, 1996; Jayasena, 1999; U.S. Pat. Nos. 5,270,163; 5,567,588;5,650,275; 5,670,637; 5,683,867; 5,696,249; 5,789,157; 5,843,653;5,864,026; 5,989,823; 6,569,630; 8,318,438 and PCT application WO99/31275, each incorporated herein by reference.

m. Ribozymes

In some embodiments, oligonucleotides provided herein may be in the formof a ribozyme. A ribozyme (ribonucleic acid enzyme) is a molecule,typically an RNA molecule, that is capable of performing specificbiochemical reactions, similar to the action of protein enzymes.Ribozymes are molecules with catalytic activities including the abilityto cleave at specific phosphodiester linkages in RNA molecules to whichthey have hybridized, such as mRNAs, RNA-containing substrates, lncRNAs,and ribozymes, themselves.

Ribozymes may assume one of several physical structures, one of which iscalled a “hammerhead.” A hammerhead ribozyme is composed of a catalyticcore containing nine conserved bases, a double-stranded stem and loopstructure (stem-loop II), and two regions complementary to the targetRNA flanking regions the catalytic core. The flanking regions enable theribozyme to bind to the target RNA specifically by formingdouble-stranded stems I and III. Cleavage occurs in cis (i.e., cleavageof the same RNA molecule that contains the hammerhead motif) or in trans(cleavage of an RNA substrate other than that containing the ribozyme)next to a specific ribonucleotide triplet by a transesterificationreaction from a 3′, 5′-phosphate diester to a 2′, 3′-cyclic phosphatediester. Without wishing to be bound by theory, it is believed that thiscatalytic activity requires the presence of specific, highly conservedsequences in the catalytic region of the ribozyme.

Modifications in ribozyme structure have also included the substitutionor replacement of various non-core portions of the molecule withnon-nucleotidic molecules. For example, Benseler et al. (J. Am. Chem.Soc. (1993) 115:8483-8484) disclosed hammerhead-like molecules in whichtwo of the base pairs of stem II, and all four of the nucleotides ofloop II were replaced with non-nucleoside linkers based on hexaethyleneglycol, propanediol, bis(triethylene glycol) phosphate,tris(propanediol)bisphosphate, or bis(propanediol) phosphate. Ma et al.(Biochem. (1993) 32:1751-1758; Nucleic Acids Res. (1993) 21:2585-2589)replaced the six nucleotide loop of the TAR ribozyme hairpin withnon-nucleotidic, ethylene glycol-related linkers. Thomson et al.(Nucleic Acids Res. (1993) 21:5600-5603) replaced loop II with linear,non-nucleotidic linkers of 13, 17, and 19 atoms in length.

Ribozyme oligonucleotides can be prepared using well known methods (see,e.g., PCT Publications WO9118624; WO9413688; WO9201806; and WO 92/07065;and U.S. Pat. Nos. 5,436,143 and 5,650,502) or can be purchased fromcommercial sources (e.g., US Biochemicals) and, if desired, canincorporate nucleotide analogs to increase the resistance of theoligonucleotide to degradation by nucleases in a cell. The ribozyme maybe synthesized in any known manner, e.g., by use of a commerciallyavailable synthesizer produced, e.g., by Applied Biosystems, Inc. orMilligen. The ribozyme may also be produced in recombinant vectors byconventional means. See, Molecular Cloning: A Laboratory Manual, ColdSpring Harbor Laboratory (Current edition). The ribozyme RNA sequencesmaybe synthesized conventionally, for example, by using RNA polymerasessuch as T7 or SP6.

n. Guide Nucleic Acids

In some embodiments, oligonucleotides are guide nucleic acid, e.g.,guide RNA (gRNA) molecules. Generally, a guide RNA is a short syntheticRNA composed of (1) a scaffold sequence that binds to a nucleic acidprogrammable DNA binding protein (napDNAbp), such as Cas9, and (2) anucleotide spacer portion that defines the DNA target sequence (e.g.,genomic DNA target) to which the gRNA binds in order to bring thenucleic acid programmable DNA binding protein in proximity to the DNAtarget sequence. In some embodiments, the napDNAbp is a nucleicacid-programmable protein that forms a complex with (e.g., binds orassociates with) one or more RNA(s) that targets the nucleicacid-programmable protein to a target DNA sequence (e.g., a targetgenomic DNA sequence). In some embodiments, a nucleic acid-programmablenuclease, when in a complex with an RNA, may be referred to as anuclease:RNA complex. Guide RNAs can exist as a complex of two or moreRNAs, or as a single RNA molecule.

Guide RNAs (gRNAs) that exist as a single RNA molecule may be referredto as single-guide RNAs (sgRNAs), though gRNA is also used to refer toguide RNAs that exist as either single molecules or as a complex of twoor more molecules. Typically, gRNAs that exist as a single RNA speciescomprise two domains: (1) a domain that shares homology to a targetnucleic acid (i.e., directs binding of a Cas9 complex to the target);and (2) a domain that binds a Cas9 protein. In some embodiments, domain(2) corresponds to a sequence known as a tracrRNA and comprises astem-loop structure. In some embodiments, domain (2) is identical orhomologous to a tracrRNA as provided in Jinek et al., Science337:816-821 (2012), the entire contents of which is incorporated hereinby reference.

In some embodiments, a gRNA comprises two or more of domains (1) and(2), and may be referred to as an extended gRNA. For example, anextended gRNA will bind two or more Cas9 proteins and bind a targetnucleic acid at two or more distinct regions, as described herein. ThegRNA comprises a nucleotide sequence that complements a target site,which mediates binding of the nuclease/RNA complex to said target site,providing the sequence specificity of the nuclease:RNA complex. In someembodiments, the RNA-programmable nuclease is the (CRISPR-associatedsystem) Cas9 endonuclease, for example, Cas9 (Csn1) from Streptococcuspyogenes (see, e.g., “Complete genome sequence of an M1 strain ofStreptococcus pyogenes.” Ferretti J. J., McShan W. M., Ajdic D. J.,Savic D. J., Savic G., Lyon K., Primeaux C., Sezate S., Suvorov A. N.,Kenton S., Lai H. S., Lin S. P., Qian Y., Jia H. G., Najar F. Z., RenQ., Zhu H., Song L., White J., Yuan X., Clifton S. W., Roe B. A.,McLaughlin R E, Proc. Natl. Acad. Sci. U.S.A. 98:4658-4663 (2001);“CRISPR RNA maturation by trans-encoded small RNA and host factor RNaseIII.” Deltcheva E., Chylinski K., Sharma C. M., Gonzales K., Chao Y.,Pirzada Z. A., Eckert M. R., Vogel J., Charpentier E., Nature471:602-607 (2011); and “A programmable dual-RNA-guided DNA endonucleasein adaptive bacterial immunity.” Jinek M., Chylinski K., Fonfara I.,Hauer M., Doudna J. A., Charpentier E. Science 337:816-821 (2012), theentire contents of each of which are incorporated herein by reference.

o. Multimers

In some embodiments, molecular payloads may comprise multimers (e.g.,concatemers) of 2 or more oligonucleotides connected by a linker. Inthis way, in some embodiments, the oligonucleotide loading of acomplex/conjugate can be increased beyond the available linking sites ona targeting agent (e.g., available thiol sites on an antibody) orotherwise tuned to achieve a particular payload loading content.Oligonucleotides in a multimer can be the same or different (e.g.,targeting different genes or different sites on the same gene orproducts thereof).

In some embodiments, multimers comprise 2 or more oligonucleotideslinked together by a cleavable linker. However, in some embodiments,multimers comprise 2 or more oligonucleotides linked together by anon-cleavable linker. In some embodiments, a multimer comprises 2, 3, 4,5, 6, 7, 8, 9, 10 or more oligonucleotides linked together. In someembodiments, a multimer comprises 2 to 5, 2 to 10 or 4 to 20oligonucleotides linked together.

In some embodiments, a multimer comprises 2 or more oligonucleotideslinked end-to-end (in a linear arrangement). In some embodiments, amultimer comprises 2 or more oligonucleotides linked end-to-end via aoligonucleotide based linker (e.g., poly-dT linker, an abasic linker).In some embodiments, a multimer comprises a 5′ end of oneoligonucleotide linked to a 3′ end of another oligonucleotide. In someembodiments, a multimer comprises a 3′ end of one oligonucleotide linkedto a 3′ end of another oligonucleotide. In some embodiments, a multimercomprises a 5′ end of one oligonucleotide linked to a 5′ end of anotheroligonucleotide. Still, in some embodiments, multimers can comprise abranched structure comprising multiple oligonucleotides linked togetherby a branching linker.

Further examples of multimers that may be used in the complexes providedherein are disclosed, for example, in US Patent Application Number2015/0315588 A1, entitled Methods of delivering multiple targetingoligonucleotides to a cell using cleavable linkers, which was publishedon Nov. 5, 2015; US Patent Application Number 2015/0247141 A1, entitledMultimeric Oligonucleotide Compounds, which was published on Sep. 3,2015, US Patent Application Number US 2011/0158937 A1, entitledImmunostimulatory Oligonucleotide Multimers, which was published on Jun.30, 2011; and U.S. Pat. No. 5,693,773, entitled Triplex-FormingAntisense Oligonucleotides Having Abasic Linkers Targeting Nucleic AcidsComprising Mixed Sequences Of Purines And Pyrimidines, which issued onDec. 2, 1997, the contents of each of which are incorporated herein byreference in their entireties.

ii. Small Molecules:

Any suitable small molecule may be used as a molecular payload, asdescribed herein. In some embodiments, the small molecule is asdescribed in US Patent Application Publication 20170340606, published onNov. 30, 2017, entitled “METHODS OF TREATING MUSCULAR DYSTROPHY” or asdescribed in US Patent Application Publication 20180050043, published onFeb. 22, 2018, entitled “INHIBITION OF DUX4 EXPRESSION USING BROMODOMAINAND EXTRA-TERMINAL DOMAIN PROTEIN INHIBITORS (BETi). Further examples ofsmall molecule payloads are provided in Bosnakovski, D., et al.,High-throughput screening identifies inhibitors of DUX4-induced myoblasttoxicity, Skelet Muscle, February 2014, and Choi. S., et al.,“Transcriptional Inhibitors Identified in a 160,000-CompoundSmall-Molecule DUX4 Viability Screen,” Journal of BiomolecularScreening, 2016. For example, in some embodiments, the small molecule isa transcriptional inhibitor, such as SHC351, SHC540, SHC572. In someembodiments, the small molecule is STR00316 increases production oractivity of another protein, such as integrin. In some embodiments, thesmall molecule is a bromodomain inhibitor (BETi), such as JQ1, PF1-1,I-BET-762, I-BET-151, RVX-208, or CPI-0610.

iii. Peptides

Any suitable peptide or protein may be used as a molecular payload, asdescribed herein. In some embodiments, a protein is an enzyme. Thesepeptides or proteins may be produced, synthesized, and/or derivatizedusing several methodologies, e.g. phage displayed peptide libraries,one-bead one-compound peptide libraries, or positional scanningsynthetic peptide combinatorial libraries. In some embodiments, thepeptide or protein may bind a DME1 or DME2 enhancer to inhibit DUX4expression, e.g., by blocking binding of an activator.

iv. Nucleic Acid Constructs

Any suitable gene expression construct may be used as a molecularpayload, as described herein. In some embodiments, a gene expressionconstruct may be a vector or a cDNA fragment. In some embodiments, agene expression construct may be messenger RNA (mRNA). In someembodiments, a mRNA used herein may be a modified mRNA, e.g., asdescribed in U.S. Pat. No. 8,710,200, issued on Apr. 24, 2014, entitled“Engineered nucleic acids encoding a modified erythropoietin and theirexpression”. In some embodiments, a mRNA may comprise a 5′ methyl cap.In some embodiments, a mRNA may comprise a polyA tail, optionally of upto 160 nucleotides in length. In some embodiments, the gene expressionconstruct may be expressed, e.g., overexpressed, within the nucleus of amuscle cell. In some embodiments, the gene expression construct encodesa oligonucleotide (e.g., an shRNA targeting DUX4) or a protein thatdownregulates the expression of DUX4 (e.g., a peptide or protein thatbinds to DME1 or DME2 enhancer to inhibit DUX4 expression, e.g., byblocking binding of an activator). In some embodiments, the geneexpression construct encodes a oligonucleotide (e.g., an shRNA targetingMuRF1 or MAFbx) that downregulates the expression of MuRF1 or MAFbx,respectively. In some embodiments, the gene expression constructsencodes a protein that comprises at least one zinc finger. In someembodiments, the gene expression construct encodes a gene editingenzyme. Additional examples of nucleic acid constructs that may be usedas molecular payloads are provided in International Patent ApplicationPublication W02017152149A1, published on Sep. 19, 2017, entitled,“CLOSED-ENDED LINEAR DUPLEX DNA FOR NON-VIRAL GENE TRANSFER”; U.S. Pat.No. 8,853,377B2, issued on Oct. 7, 2014, entitled, “MRNA FOR USE INTREATMENT OF HUMAN GENETIC DISEASES”; and U.S. Pat. No. 8,822,663B2,issued on Sep. 2, 2014, ENGINEERED NUCLEIC ACIDS AND METHODS OF USETHEREOF,” the contents of each of which are incorporated herein byreference in their entireties.

C. Linkers

Complexes described herein generally comprise a linker that connects amuscle-targeting agent to a molecular payload. A linker comprises atleast one covalent bond. In some embodiments, a linker may be a singlebond, e.g., a disulfide bond or disulfide bridge, that connects amuscle-targeting agent to a molecular payload. However, in someembodiments, a linker may connect a muscle-targeting agent to amolecular payload through multiple covalent bonds. In some embodiments,a linker may be a cleavable linker. However, in some embodiments, alinker may be a non-cleavable linker. A linker is generally stable invitro and in vivo, and may be stable in certain cellular environments.Additionally, generally a linker does not negatively impact thefunctional properties of either the muscle-targeting agent or themolecular payload. Examples and methods of synthesis of linkers areknown in the art (see, e.g. Kline, T. et al. “Methods to Make HomogenousAntibody Drug Conjugates.” Pharmaceutical Research, 2015, 32:11,3480-3493.; Jain, N. et al. “Current ADC Linker Chemistry” Pharm Res.2015, 32:11, 3526-3540.; McCombs, J. R. and Owen, S. C. “Antibody DrugConjugates: Design and Selection of Linker, Payload and ConjugationChemistry” AAPS J. 2015, 17:2, 339-351.).

A precursor to a linker typically will contain two different reactivespecies that allow for attachment to both the muscle-targeting agent anda molecular payload. In some embodiments, the two different reactivespecies may be a nucleophile and/or an electrophile. In someembodiments, a linker is connected to a muscle-targeting agent viaconjugation to a lysine residue or a cysteine residue of themuscle-targeting agent. In some embodiments, a linker is connected to acysteine residue of a muscle-targeting agent via a maleimide-containinglinker, wherein optionally the maleimide-containing linker comprises amaleimidocaproyl or maleimidomethyl cyclohexane-1-carboxylate group. Insome embodiments, a linker is connected to a cysteine residue of amuscle-targeting agent or thiol functionalized molecular payload via a3-arylpropionitrile functional group. In some embodiments, a linker isconnected to a muscle-targeting agent and/or a molecular payload via anamide bond, a hydrazide, a triazole, a thioether or a disulfide bond.

i. Cleavable Linkers

A cleavable linker may be a protease-sensitive linker, a pH-sensitivelinker, or a glutathione-sensitive linker. These linkers are generallycleavable only intracellularly and are preferably stable inextracellular environments, e.g. extracellular to a muscle cell.

Protease-sensitive linkers are cleavable by protease enzymatic activity.These linkers typically comprise peptide sequences and may be 2-10 aminoacids, about 2-5 amino acids, about 5-10 amino acids, about 10 aminoacids, about 5 amino acids, about 3 amino acids, or about 2 amino acidsin length. In some embodiments, a peptide sequence may comprisenaturally-occurring amino acids, e.g. cysteine, alanine, ornon-naturally-occurring or modified amino acids. Non-naturally occurringamino acids include β-amino acids, homo-amino acids, prolinederivatives, 3-substituted alanine derivatives, linear core amino acids,N-methyl amino acids, and others known in the art. In some embodiments,a protease-sensitive linker comprises a valine-citrulline oralanine-citrulline dipeptide sequence. In some embodiments, aprotease-sensitive linker can be cleaved by a lysosomal protease, e.g.cathepsin B, and/or an endosomal protease.

A pH-sensitive linker is a covalent linkage that readily degrades inhigh or low pH environments. In some embodiments, a pH-sensitive linkermay be cleaved at a pH in a range of 4 to 6. In some embodiments, apH-sensitive linker comprises a hydrazone or cyclic acetal. In someembodiments, a pH-sensitive linker is cleaved within an endosome or alysosome.

In some embodiments, a glutathione-sensitive linker comprises adisulfide moiety. In some embodiments, a glutathione-sensitive linker iscleaved by an disulfide exchange reaction with a glutathione speciesinside a cell. In some embodiments, the disulfide moiety furthercomprises at least one amino acid, e.g. a cysteine residue.

In some embodiments, the linker is a Val-cit linker (e.g., as describedin U.S. Pat. No. 6,214,345, incorporated herein by reference). In someembodiments, before conjugation, the val-cit linker has a structure of:

In some embodiments, after conjugation, the val-cit linker has astructure of:

ii. Non-Cleavable Linkers

In some embodiments, non-cleavable linkers may be used. Generally, anon-cleavable linker cannot be readily degraded in a cellular orphysiological environment. In some embodiments, a non-cleavable linkercomprises an optionally substituted alkyl group, wherein thesubstitutions may include halogens, hydroxyl groups, oxygen species, andother common substitutions. In some embodiments, a linker may comprisean optionally substituted alkyl, an optionally substituted alkylene, anoptionally substituted arylene, a heteroarylene, a peptide sequencecomprising at least one non-natural amino acid, a truncated glycan, asugar or sugars that cannot be enzymatically degraded, an azide, analkyne-azide, a peptide sequence comprising a LPXT sequence, athioether, a biotin, a biphenyl, repeating units of polyethylene glycolor equivalent compounds, acid esters, acid amides, sulfamides, and/or analkoxy-amine linker. In some embodiments, sortase-mediated ligation willbe utilized to covalently link a muscle-targeting agent comprising aLPXT sequence to a molecular payload comprising a (G)_(n) sequence (see,e.g. Proft T. Sortase-mediated protein ligation: an emergingbiotechnology tool for protein modification and immobilization.Biotechnol Lett. 2010, 32(1):1-10.).

In some embodiments, a linker may comprise a substituted alkylene, anoptionally substituted alkenylene, an optionally substituted alkynylene,an optionally substituted cycloalkylene, an optionally substitutedcycloalkenylene, an optionally substituted arylene, an optionallysubstituted heteroarylene further comprising at least one heteroatomselected from N, O, and S, an optionally substituted heterocyclylenefurther comprising at least one heteroatom selected from N, O, and S, animino, an optionally substituted nitrogen species, an optionallysubstituted oxygen species O, an optionally substituted sulfur species,or a poly(alkylene oxide), e.g. polyethylene oxide or polypropyleneoxide.

iii. Linker conjugation

In some embodiments, a linker is connected to a muscle-targeting agentand/or molecular payload via a phosphate, thioether, ether,carbon-carbon, or amide bond. In some embodiments, a linker is connectedto an oligonucleotide through a phosphate or phosphorothioate group,e.g. a terminal phosphate of an oligonucleotide backbone. In someembodiments, a linker is connected to an muscle-targeting agent, e.g. anantibody, through a lysine or cysteine residue present on themuscle-targeting agent

In some embodiments, a linker is connected to a muscle-targeting agentand/or molecular payload by a cycloaddition reaction between an azideand an alkyne to form a triazole, wherein the azide and the alkyne maybe located on the muscle-targeting agent, molecular payload, or thelinker. In some embodiments, an alkyne may be a cyclic alkyne, e.g., acyclooctyne. In some embodiments, an alkyne may be bicyclononyne (alsoknown as bicyclo[6.1.0]nonyne or BCN) or substituted bicyclononyne. Insome embodiments, a cyclooctane is as described in International PatentApplication Publication WO2011136645, published on Nov. 3, 2011,entitled, “Fused Cyclooctyne Compounds And Their Use In Metal free ClickReactions”. In some embodiments, an azide may be a sugar or carbohydratemolecule that comprises an azide. In some embodiments, an azide may be6-azido-6-deoxygalactose or 6-azido-N-acetylgalactosamine. In someembodiments, a sugar or carbohydrate molecule that comprises an azide isas described in International Patent Application PublicationWO2016170186, published on Oct. 27, 2016, entitled, “Process For TheModification Of A Glycoprotein Using A Glycosyltransferase That Is Or IsDerived From A β(1,4)-N-Acetylgalactosaminyltransferase”. In someembodiments, a cycloaddition reaction between an azide and an alkyne toform a triazole, wherein the azide and the alkyne may be located on themuscle-targeting agent, molecular payload, or the linker is as describedin International Patent Application Publication WO2014065661, publishedon May 1, 2014, entitled, “Modified antibody, antibody-conjugate andprocess for the preparation thereof”; or International PatentApplication Publication WO2016170186, published on Oct. 27, 2016,entitled, “Process For The Modification Of A Glycoprotein Using AGlycosyltransferase That Is Or Is Derived From A β(1,4)-N-A cetylgalactosaminyltransferase”.

In some embodiments, a linker further comprises a spacer, e.g., apolyethylene glycol spacer or an acyl/carbomoyl sulfamide spacer, e.g.,a HydraSpace™ spacer. In some embodiments, a spacer is as described inVerkade, J. M. M. et al., “A Polar Sulfamide Spacer SignificantlyEnhances the Manufacturability, Stability, and Therapeutic Index ofAntibody-Drug Conjugates”, Antibodies, 2018, 7, 12.

In some embodiments, a linker is connected to a muscle-targeting agentand/or molecular payload by the Diels-Alder reaction between adienophile and a diene/hetero-diene, wherein the dienophile and thediene/hetero-diene may be located on the muscle-targeting agent,molecular payload, or the linker. In some embodiments a linker isconnected to a muscle-targeting agent and/or molecular payload by otherpericyclic reactions, e.g. ene reaction. In some embodiments, a linkeris connected to a muscle-targeting agent and/or molecular payload by anamide, thioamide, or sulfonamide bond reaction. In some embodiments, alinker is connected to a muscle-targeting agent and/or molecular payloadby a condensation reaction to form an oxime, hydrazone, or semicarbazidegroup existing between the linker and the muscle-targeting agent and/ormolecular payload.

In some embodiments, a linker is connected to a muscle-targeting agentand/or molecular payload by a conjugate addition reactions between anucleophile, e.g. an amine or a hydroxyl group, and an electrophile,e.g. a carboxylic acid or an aldehyde. In some embodiments, anucleophile may exist on a linker and an electrophile may exist on amuscle-targeting agent or molecular payload prior to a reaction betweena linker and a muscle-targeting agent or molecular payload. In someembodiments, an electrophile may exist on a linker and a nucleophile mayexist on a muscle-targeting agent or molecular payload prior to areaction between a linker and a muscle-targeting agent or molecularpayload. In some embodiments, an electrophile may be an azide, a siliconcenters, a carbonyl, a carboxylic acid, an anhydride, an isocyanate, athioisocyanate, a succinimidyl ester, a sulfosuccinimidyl ester, amaleimide, an alkyl halide, an alkyl pseudohalide, an epoxide, anepisulfide, an aziridine, an aryl, an activated phosphorus center,and/or an activated sulfur center. In some embodiments, a nucleophilemay be an optionally substituted alkene, an optionally substitutedalkyne, an optionally substituted aryl, an optionally substitutedheterocyclyl, a hydroxyl group, an amino group, an alkylamino group, ananilido group, or a thiol group.

D. Examples of Antibody-Molecular Payload Complexes

Other aspects of the present disclosure provide complexes comprising anyone the muscle targeting agent (e.g., a transferrin receptor antibodies)described herein covalently linked to any of the molecular payloads(e.g., an oligonucleotide) described herein. In some embodiments, themuscle targeting agent (e.g., a transferrin receptor antibody) iscovalently linked to a molecular payload (e.g., an oligonucleotide) viaa linker. Any of the linkers described herein may be used. In someembodiments, the linker is linked to the 5′ end, the 3′ end, orinternally of the oligonucleotide. In some embodiments, the linker islinked to the antibody via a thiol-reactive linkage (e.g., via acysteine in the antibody).

An exemplary structure of a complex comprising a transferrin receptorantibody covalently linked to an oligonucleotide via a Val-cit linker isprovided below:

wherein the linker is linked to the 5′ end, the 3′ end, or internally ofthe oligonucleotide, and wherein the linker is linked to the antibodyvia a thiol-reactive linkage (e.g., via a cysteine in the antibody).

It should be appreciated that antibodies can be linked tooligonucleotides with different stochiometries, a property that may bereferred to as a drug to antibody ratios (DAR) with the “drug” being theoligonucleotide. In some embodiments, one oligonucleotide is linked toan antibody (DAR=1). In some embodiments, two oligonucleotides arelinked to an antibody (DAR=2). In some embodiments, threeoligonucleotides are linked to an antibody (DAR=3). In some embodiments,four oligonucleotides are linked to an antibody (DAR=4). In someembodiments, a mixture of different complexes, each having a differentDAR, is provided. In some embodiments, an average DAR of complexes insuch a mixture may be in a range of 1 to 3, 1 to 4, 1 to 5 or more. DARmay be increased by conjugating oligonucleotides to different sites onan antibody and/or by conjugating multimers to one or more sites onantibody. For example, a DAR of 2 may be achieved by conjugating asingle oligonucleotide to two different sites on an antibody or byconjugating a dimer oligonucleotide to a single site of an antibody.

In some embodiments, the complex described herein comprises atransferrin receptor antibody (e.g., an antibody or any variant thereofas described herein) covalently linked to an oligonucleotide. In someembodiments, the complex described herein comprises a transferrinreceptor antibody (e.g., an antibody or any variant thereof as describedherein) covalently linked to an oligonucleotide via a linker (e.g., aVal-cit linker). In some embodiments, the linker (e.g., a Val-citlinker) is linked to the 5′ end, the 3′ end, or internally of theoligonucleotide. In some embodiments, the linker (e.g., a Val-citlinker) is linked to the antibody (e.g., an antibody or any variantthereof as described herein) via a thiol-reactive linkage (e.g., via acysteine in the antibody).

In some embodiments, the complex described herein comprises atransferrin receptor antibody covalently linked to an oligonucleotide,wherein the transferrin receptor antibody comprises a CDR-H1, a CDR-H2,and a CDR-H3 that are the same as the CDR-H1, CDR-H2, and CDR-H3 shownin Table 1.1; and a CDR-L1, a CDR-L2, and a CDR-L3 that are the same asthe CDR-L1, CDR-L2, and CDR-L3 shown in Table 1.1.

In some embodiments, the complex described herein comprises atransferrin receptor antibody covalently linked to an oligonucleotide,wherein the transferrin receptor antibody comprises a VH having theamino acid sequence of SEQ ID NO: 33 and a VL having the amino acidsequence of SEQ ID NO: 34. In some embodiments, the complex describedherein comprises a transferrin receptor antibody covalently linked to anoligonucleotide, wherein the transferrin receptor antibody comprises aVH having the amino acid sequence of SEQ ID NO: 35 and a VL having theamino acid sequence of SEQ ID NO: 36.

In some embodiments, the complex described herein comprises atransferrin receptor antibody covalently linked to an oligonucleotide,wherein the transferrin receptor antibody comprises a heavy chain havingthe amino acid sequence of SEQ ID NO: 39 and a light chain having theamino acid sequence of SEQ ID NO: 40. In some embodiments, the complexdescribed herein comprises a transferrin receptor antibody covalentlylinked to an oligonucleotide, wherein the transferrin receptor antibodycomprises a heavy chain having the amino acid sequence of SEQ ID NO: 41and a light chain having the amino acid sequence of SEQ ID NO: 42.

In some embodiments, the complex described herein comprises atransferrin receptor antibody covalently linked to an oligonucleotidevia a linker (e.g., a Val-cit linker), wherein the transferrin receptorantibody comprises a CDR-H1, a CDR-H2, and a CDR-H3 that are the same asthe CDR-H1, CDR-H2, and CDR-H3 shown in Table 1.1; and a CDR-L1, aCDR-L2, and a CDR-L3 that are the same as the CDR-L1, CDR-L2, and CDR-L3shown in Table 1.1.

In some embodiments, the complex described herein comprises atransferrin receptor antibody covalently linked to an oligonucleotidevia a linker (e.g., a Val-cit linker), wherein the transferrin receptorantibody comprises a VH having the amino acid sequence of SEQ ID NO: 33and a VL having the amino acid sequence of SEQ ID NO: 34. In someembodiments, the complex described herein comprises a transferrinreceptor antibody covalently linked to an oligonucleotide via a linker(e.g., a Val-cit linker), wherein the transferrin receptor antibodycomprises a VH having the amino acid sequence of SEQ ID NO: 35 and a VLhaving the amino acid sequence of SEQ ID NO: 36.

In some embodiments, the complex described herein comprises atransferrin receptor antibody covalently linked to an oligonucleotidevia a linker (e.g., a Val-cit linker), wherein the transferrin receptorantibody comprises a heavy chain having the amino acid sequence of SEQID NO: 39 and a light chain having the amino acid sequence of SEQ ID NO:40. In some embodiments, the complex described herein comprises atransferrin receptor antibody covalently linked to an oligonucleotidevia a linker (e.g., a Val-cit linker), wherein the transferrin receptorantibody comprises a heavy chain having the amino acid sequence of SEQID NO: 41 and a light chain having the amino acid sequence of SEQ ID NO:42.

In some embodiments, the complex described herein comprises atransferrin receptor antibody covalently linked to an oligonucleotidevia a Val-cit linker, wherein the transferrin receptor antibodycomprises a CDR-H1, a CDR-H2, and a CDR-H3 that are the same as theCDR-H1, CDR-H2, and CDR-H3 shown in Table 1.1; and a CDR-L1, a CDR-L2,and a CDR-L3 that are the same as the CDR-L1, CDR-L2, and CDR-L3 shownin Table 1.1, and wherein the complex comprises the structure of:

wherein the linker Val-cit linker is linked to the 5′ end, the 3′ end,or internally of the oligonucleotide, and wherein the Val-cit linker islinked to the antibody (e.g., an antibody or any variant thereof asdescribed herein) via a thiol-reactive linkage (e.g., via a cysteine inthe antibody).

In some embodiments, the complex described herein comprises atransferrin receptor antibody covalently linked to an oligonucleotidevia a Val-cit linker, wherein the transferrin receptor antibodycomprises a VH having the amino acid sequence of SEQ ID NO: 33 and a VLhaving the amino acid sequence of SEQ ID NO: 34, and wherein the complexcomprises the structure of:

wherein the linker Val-cit linker is linked to the 5′ end, the 3′ end,or internally of the oligonucleotide, and wherein the Val-cit linker islinked to the antibody (e.g., an antibody or any variant thereof asdescribed herein) via a thiol-reactive linkage (e.g., via a cysteine inthe antibody).

In some embodiments, the complex described herein comprises atransferrin receptor antibody covalently linked to an oligonucleotidevia a Val-cit linker, wherein the transferrin receptor antibodycomprises a VH having the amino acid sequence of SEQ ID NO: 35 and a VLhaving the amino acid sequence of SEQ ID NO: 36, and wherein the complexcomprises the structure of:

wherein the linker Val-cit linker is linked to the 5′ end, the 3′ end,or internally of the oligonucleotide, and wherein the Val-cit linker islinked to the antibody (e.g., an antibody or any variant thereof asdescribed herein) via a thiol-reactive linkage (e.g., via a cysteine inthe antibody).

In some embodiments, the complex described herein comprises atransferrin receptor antibody covalently linked to an oligonucleotidevia a Val-cit linker, wherein the transferrin receptor antibodycomprises a heavy chain having the amino acid sequence of SEQ ID NO: 39and a light chain having the amino acid sequence of SEQ ID NO: 40, andwherein the complex comprises the structure of:

wherein the linker Val-cit linker is linked to the 5′ end, the 3′ end,or internally of an oligonucleotide, and wherein the Val-cit linker islinked to the antibody (e.g., an antibody or any variant thereof asdescribed herein) via a thiol-reactive linkage (e.g., via a cysteine inthe antibody).

In some embodiments, the complex described herein comprises atransferrin receptor antibody covalently linked to an oligonucleotidevia a Val-cit linker, wherein the transferrin receptor antibodycomprises a heavy chain having the amino acid sequence of SEQ ID NO: 41and a light chain having the amino acid sequence of SEQ ID NO: 42, andwherein the complex comprises the structure of:

wherein the linker Val-cit linker is linked to the 5′ end, the 3′ end,or internally of an oligonucleotide, and wherein the Val-cit linker islinked to the antibody (e.g., an antibody or any variant thereof asdescribed herein) via a thiol-reactive linkage (e.g., via a cysteine inthe antibody).

III. Formulations

Complexes provided herein may be formulated in any suitable mannerGenerally, complexes provided herein are formulated in a manner suitablefor pharmaceutical use. For example, complexes can be delivered to asubject using a formulation that minimizes degradation, facilitatesdelivery and/or uptake, or provides another beneficial property to thecomplexes in the formulation. In some embodiments, provided herein arecompositions comprising complexes and pharmaceutically acceptablecarriers. Such compositions can be suitably formulated such that whenadministered to a subject, either into the immediate environment of atarget cell or systemically, a sufficient amount of the complexes entertarget muscle cells. In some embodiments, complexes are formulated inbuffer solutions such as phosphate-buffered saline solutions, liposomes,micellar structures, and capsids.

It should be appreciated that, in some embodiments, compositions mayinclude separately one or more components of complexes provided herein(e.g., muscle-targeting agents, linkers, molecular payloads, orprecursor molecules of any one of them).

In some embodiments, complexes are formulated in water or in an aqueoussolution (e.g., water with pH adjustments). In some embodiments,complexes are formulated in basic buffered aqueous solutions (e.g.,PBS). In some embodiments, formulations as disclosed herein comprise anexcipient. In some embodiments, an excipient confers to a compositionimproved stability, improved absorption, improved solubility and/ortherapeutic enhancement of the active ingredient. In some embodiments,an excipient is a buffering agent (e.g., sodium citrate, sodiumphosphate, a tris base, or sodium hydroxide) or a vehicle (e.g., abuffered solution, petrolatum, dimethyl sulfoxide, or mineral oil).

In some embodiments, a complex or component thereof (e.g.,oligonucleotide or antibody) is lyophilized for extending its shelf-lifeand then made into a solution before use (e.g., administration to asubject). Accordingly, an excipient in a composition comprising acomplex, or component thereof, described herein may be a lyoprotectant(e.g., mannitol, lactose, polyethylene glycol, or polyvinyl pyrolidone),or a collapse temperature modifier (e.g., dextran, ficoll, or gelatin).

In some embodiments, a pharmaceutical composition is formulated to becompatible with its intended route of administration. Examples of routesof administration include parenteral, e.g., intravenous, intradermal,subcutaneous, administration. Typically, the route of administration isintravenous or subcutaneous.

Pharmaceutical compositions suitable for injectable use include sterileaqueous solutions (where water soluble) or dispersions and sterilepowders for the extemporaneous preparation of sterile injectablesolutions or dispersions. The carrier can be a solvent or dispersionmedium containing, for example, water, ethanol, polyol (for example,glycerol, propylene glycol, and liquid polyethylene glycol, and thelike), and suitable mixtures thereof. In some embodiments, formulationsinclude isotonic agents, for example, sugars, polyalcohols such asmannitol, sorbitol, and sodium chloride in the composition. Sterileinjectable solutions can be prepared by incorporating the a complexes ina required amount in a selected solvent with one or a combination ofingredients enumerated above, as required, followed by filteredsterilization.

In some embodiments, a composition may contain at least about 0.1% ofthe a complex, or component thereof, or more, although the percentage ofthe active ingredient(s) may be between about 1% and about 80% or moreof the weight or volume of the total composition. Factors such assolubility, bioavailability, biological half-life, route ofadministration, product shelf life, as well as other pharmacologicalconsiderations will be contemplated by one skilled in the art ofpreparing such pharmaceutical formulations, and as such, a variety ofdosages and treatment regimens may be desirable.

IV. Methods of Use/Treatment

Complexes comprising a muscle-targeting agent covalently to a molecularpayload as described herein are effective in treating FSHD. In someembodiments, complexes are effective in treating Type I FSHD. In someembodiments, complexes are effective in treating Type II FSHD. In someembodiments, FSHD is associated with deletions in D4Z4 repeat regions onchromosome 4 which contain the DUX4 gene. In some embodiments, FSHD isassociated with mutations in the SMCHD1 gene.

In some embodiments, a subject may be a human subject, a non-humanprimate subject, a rodent subject, or any suitable mammalian subject. Insome embodiments, a subject may have myotonic dystrophy. In someembodiments, a subject has elevated expression of the DUX4 gene outsideof fetal development and the testes. In some embodiments, the subjecthas facioscapulohumeral muscular dystrophy of Type I or Type II. In someembodiments, the subject having FSHD has mutations in the SMCHD1 gene.In some embodiments, the subject having FSHD has deletion mutations inD4Z4 repeat regions on chromosome 4.

An aspect of the disclosure includes a methods involving administeringto a subject an effective amount of a complex as described herein. Insome embodiments, an effective amount of a pharmaceutical compositionthat comprises a complex comprising a muscle-targeting agent covalentlyto a molecular payload can be administered to a subject in need oftreatment. In some embodiments, a pharmaceutical composition comprisinga complex as described herein may be administered by a suitable route,which may include intravenous administration, e.g., as a bolus or bycontinuous infusion over a period of time. In some embodiments,intravenous administration may be performed by intramuscular,intraperitoneal, intracerebrospinal, subcutaneous, intra-articular,intrasynovial, or intrathecal routes. In some embodiments, apharmaceutical composition may be in solid form, aqueous form, or aliquid form. In some embodiments, an aqueous or liquid form may benebulized or lyophilized. In some embodiments, a nebulized orlyophilized form may be reconstituted with an aqueous or liquidsolution.

Compositions for intravenous administration may contain various carrierssuch as vegetable oils, dimethylactamide, dimethyformamide, ethyllactate, ethyl carbonate, isopropyl myristate, ethanol, and polyols(glycerol, propylene glycol, liquid polyethylene glycol, and the like).For intravenous injection, water soluble antibodies can be administeredby the drip method, whereby a pharmaceutical formulation containing theantibody and a physiologically acceptable excipients is infused.Physiologically acceptable excipients may include, for example, 5%dextrose, 0.9% saline, Ringer's solution or other suitable excipients.Intramuscular preparations, e.g., a sterile formulation of a suitablesoluble salt form of the antibody, can be dissolved and administered ina pharmaceutical excipient such as Water-for-Injection, 0.9% saline, or5% glucose solution.

In some embodiments, a pharmaceutical composition that comprises acomplex comprising a muscle-targeting agent covalently to a molecularpayload is administered via site-specific or local delivery techniques.Examples of these techniques include implantable depot sources of thecomplex, local delivery catheters, site specific carriers, directinjection, or direct application.

In some embodiments, a pharmaceutical composition that comprises acomplex comprising a muscle-targeting agent covalently to a molecularpayload is administered at an effective concentration that conferstherapeutic effect on a subject. Effective amounts vary, as recognizedby those skilled in the art, depending on the severity of the disease,unique characteristics of the subject being treated, e.g. age, physicalconditions, health, or weight, the duration of the treatment, the natureof any concurrent therapies, the route of administration and relatedfactors. These related factors are known to those in the art and may beaddressed with no more than routine experimentation. In someembodiments, an effective concentration is the maximum dose that isconsidered to be safe for the patient. In some embodiments, an effectiveconcentration will be the lowest possible concentration that providesmaximum efficacy.

Empirical considerations, e.g. the half-life of the complex in asubject, generally will contribute to determination of the concentrationof pharmaceutical composition that is used for treatment. The frequencyof administration may be empirically determined and adjusted to maximizethe efficacy of the treatment.

Generally, for administration of any of the complexes described herein,an initial candidate dosage may be about 1 to 100 mg/kg, or more,depending on the factors described above, e.g. safety or efficacy. Insome embodiments, a treatment will be administered once. In someembodiments, a treatment will be administered daily, biweekly, weekly,bimonthly, monthly, or at any time interval that provide maximumefficacy while minimizing safety risks to the subject. Generally, theefficacy and the treatment and safety risks may be monitored throughoutthe course of treatment.

The efficacy of treatment may be assessed using any suitable methods. Insome embodiments, the efficacy of treatment may be assessed byevaluation of observation of symptoms associated with FSHD includingmuscle mass loss and muscle atrophy, primarily in the muscles of theface, shoulder blades, and upper arms.

In some embodiments, a pharmaceutical composition that comprises acomplex comprising a muscle-targeting agent covalently to a molecularpayload described herein is administered to a subject at an effectiveconcentration sufficient to inhibit activity or expression of a targetgene by at least 10%, at least 20%, at least 30%, at least 40%, at least50%, at least 60%, at least 70%, at least 80%, at least 90% or at least95% relative to a control, e.g. baseline level of gene expression priorto treatment.

In some embodiments, a single dose or administration of a pharmaceuticalcomposition that comprises a complex comprising a muscle-targeting agentcovalently to a molecular payload described herein to a subject issufficient to inhibit activity or expression of a target gene for atleast 1-5, 1-10, 5-15, 10-20, 15-30, 20-40, 25-50, or more days. In someembodiments, a single dose or administration of a pharmaceuticalcomposition that comprises a complex comprising a muscle-targeting agentcovalently to a molecular payload described herein to a subject issufficient to inhibit activity or expression of a target gene for atleast 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 weeks. In someembodiments, a single dose or administration of a pharmaceuticalcomposition that comprises a complex comprising a muscle-targeting agentcovalently to a molecular payload described herein to a subject issufficient to inhibit activity or expression of a target gene for atleast 1, 2, 3, 4, 5, or 6 months.

In some embodiments, a pharmaceutical composition may comprises morethan one complex comprising a muscle-targeting agent covalently to amolecular payload. In some embodiments, a pharmaceutical composition mayfurther comprise any other suitable therapeutic agent for treatment of asubject, e.g. a human subject having FSHD. In some embodiments, theother therapeutic agents may enhance or supplement the effectiveness ofthe complexes described herein. In some embodiments, the othertherapeutic agents may function to treat a different symptom or diseasethan the complexes described herein.

EXAMPLES Example 1: Targeting Gene Expression with Transfected AntisenseOligonucleotides

A siRNA that targets hypoxanthine phosphoribosyltransferase (HPRT) wastested in vitro for its ability to reduce expression levels of HPRT inan immortalized cell line. Briefly, Hepa 1-6 cells were transfected witheither a control siRNA (siCTRL; 100 nM) or the siRNA that targets HPRT(siHPRT; 100 nM), formulated with lipofectamine 2000. HPRT expressionlevels were evaluated 48 hours following transfection. A controlexperiment was also performed in which vehicle (phosphate-bufferedsaline) was delivered to Hepa 1-6 cells in culture and the cells weremaintained for 48 hours. As shown in FIG. 1, it was found that the HPRTsiRNA reduced HPRT expression levels by ˜90% compared with controls.

TABLE 2 Sequences of siHPRT and siCTRL Sequence SiHPRT5′-UcCuAuGaCuGuAgAu sense UuUaU-(CH₂)₆NH₂-3′ strand siHPRT 5′-paUaAaAuCuAcAgUc antisense AuAgGasAsu-3′ strand siCTRL 5′-UgUaAuAaCcAuAuCuA sense cCuU-(CH₂)₆NH₂-3′ strand SiCTRL5′-aAgGuAgAuAuGgUuAu Antisense UaCasAsa-3′ strand *Lower case-2′Omeribose; Capital letter-2′Fluoro ribose; p-phosphate linkage;s-phosphorothioate linkage

Example 2: Targeting HPRT with a Muscle-Targeting Complex

A muscle-targeting complex was generated comprising the HPRT siRNA usedin Example 1 (siHPRT) covalently linked, via a non-cleavableN-gamma-maleimidobutyryl-oxysuccinimide ester (GMBS) linker, toDTX-A-002, an anti-transferrin receptor antibody.

Briefly, the GMBS linker was dissolved in dry DMSO and coupled to the 3′end of the sense strand of siHPRT through amide bond formation underaqueous conditions. Completion of the reaction was verified by Kaisertest. Excess linker and organic solvents were removed by gel permeationchromatography. The purified, maleimide functionalized sense strand ofsiHPRT was then coupled to DTX-A-002 antibody using a Michael additionreaction.

The product of the antibody coupling reaction was then subjected tohydrophobic interaction chromatography (HIC-HPLC). antiTfR-siHPRTcomplexes comprising one or two siHPRT molecules covalently attached toDTX-A-002 antibody were purified. Densitometry confirmed that thepurified sample of complexes had an average siHPRT to antibody ratio of1.46. SDS-PAGE analysis demonstrated that >90% of the purified sample ofcomplexes comprised DTX-A-002 linked to either one or two siHPRTmolecules.

Using the same methods as described above, a control IgG2a-siHPRTcomplex was generated comprising the HPRT siRNA used in Example 1(siHPRT) covalently linked via the GMBS linker to an IgG2a (Fab)antibody (DTX-A-003). Densitometry confirmed that DTX-C-001 had anaverage siHPRT to antibody ratio of 1.46 and SDS-PAGE demonstratedthat >90% of the purified sample of control complexes comprisedDTX-A-003 linked to either one or two siHPRT molecules.

The antiTfR-siHPRT complex was then tested for cellular internalizationand inhibition of HPRT in cellulo. Hepa 1-6 cells, which have relativelyhigh expression levels of transferrin receptor, were incubated in thepresence of vehicle (phosphate-buffered saline), IgG2a-siHPRT (100 nM),antiTfR-siCTRL (100 nM), or antiTfR-siHPRT (100 nM), for 72 hours. Afterthe 72 hour incubation, the cells were isolated and assayed forexpression levels of HPRT (FIG. 2). Cells treated with theantiTfR-siHPRT demonstrated a reduction in HPRT expression by ˜50%relative to the cells treated with the vehicle control. Meanwhile, cellstreated with either of the IgG2a-siHPRT or antiTfR-siCTRL had HPRTexpression levels comparable to the vehicle control (no reduction inHPRT expression). These data indicate that the anti-transferrin receptorantibody of the antiTfR-siHPRT enabled cellular internalization of thecomplex, thereby allowing the siHPRT to inhibit expression of HPRT.

Example 3: Targeting HPRT in Mouse Muscle Tissues with aMuscle-Targeting Complex

The muscle-targeting complex described in Example 2, antiTfR-siHPRT, wastested for inhibition of HPRT in mouse tissues. C57BL/6 wild-type micewere intravenously injected with a single dose of a vehicle control(phosphate-buffered saline); siHPRT (2 mg/kg of RNA); IgG2a-siHPRT (2mg/kg of RNA, corresponding to 9 mg/kg antibody complex); orantiTfR-siHPRT (2 mg/kg of RNA, corresponding to 9 mg/kg antibodycomplex. Each experimental condition was replicated in four individualC57BL/6 wild-type mice. Following a three-day period after injection,the mice were euthanized and segmented into isolated tissue types.Individual tissue samples were subsequently assayed for expressionlevels of HPRT (FIGS. 3A-3B and 4A-4E).

Mice treated with the antiTfR-siHPRT complex demonstrated a reduction inHPRT expression in gastrocnemius (31% reduction; p<0.05) and heart (30%reduction; p<0.05), relative to the mice treated with the siHPRT control(FIGS. 3A-3B). Meanwhile, mice treated with the IgG2a-siHPRT complex hadHPRT expression levels comparable to the siHPRT control (little or noreduction in HPRT expression) for all assayed muscle tissue types.

Mice treated with the antiTfR-siHPRT complex demonstrated no change inHPRT expression in non-muscle tissues such as brain, liver, lung,kidney, and spleen tissues (FIGS. 4A-4E).

These data indicate that the anti-transferrin receptor antibody of theantiTfR-siHPRT complex enabled cellular internalization of the complexinto muscle-specific tissues in an in vivo mouse model, thereby allowingthe siHPRT to inhibit expression of HPRT. These data further demonstratethat the antiTfR-oligonucleotide complexes of the current disclosure arecapable of specifically targeting muscle tissues.

Example 4: Targeting DUX4 with Transfected Antisense Oligonucleotides

Three DUX4-expressing cell lines (A549, U-2 OS, and HepG2 cell lines)and immortalized skeletal muscle myoblasts (SkMC) were screened forexpression of DUX4 mRNA (FIG. 5). Cells were seeded at a density of10,000 cells/well and harvested for total RNA. cDNA was synthesized fromthe total RNA extracts and qPCR was performed to determine concentrationof DUX4 relative to a control gene (PPIB) in technical quadruplicate.These data were used to aid in the selection of the U-2 OS cell line fordownstream development of DUX4-targeting oligonucleotides.

Following selection of U-2 OS cells for development of DUX4-targetingoligonucleotides, a phosphorodiamidate morpholino oligomer (PMO) versionof an antisense oligonucleotide that targets DUX4 (FM10 PMO) wasevaluated for its ability to target DUX4 in vitro. FM10 PMO comprisesthe sequence GGGCATTTTAATATATCTCTGAACT (SEQ ID NO: 45). A controlphosphorodiamidate morpholino oligomer (PMO), that comprises thesequence CCTCTTACCTCAGTTACAATTTATA, was utilized as a negative control.

Briefly, U-2 OS cells were seeded at a density of 10 k cells/well beforebeing allowed to recover overnight. Cells were then treated with eithera control PMO (100 nM) or with the FM10 PMO (10 μM). Cells wereincubated for 72 hours before being harvested for total RNA. cDNA wasthen synthesized from the total RNA extracts and qPCR was performed todetermine expression of downstream DUX4 genes (ZSCAN1, MBDL3L2, TRIM43)in technical quadruplicate. All qPCR data were analyzed using a standardAACT method and were normalized to a plate-based negative controlcomprised of untreated cells (i.e., without any oligonucleotide).Results were then converted to fold change to evaluate efficacy.

As shown in FIG. 6, all of ZSCAN1, MBDL3L2, and TRIM43 showed decreasedexpression in the presence of the FM10 PMO compared to the control PMO(42%, 34%, and 32%; respectively). These data demonstrate that the FM10PMO is capable of targeting DUX4 in vitro.

Example 5: Targeting DUX4 with a Muscle-Targeting Complex

A muscle-targeting complex is generated comprising an antisenseoligonucleotide that targets a mutant allele of DUX4 (DUX4 ASO)covalently linked, via a cathepsin cleavable linker, to DTX-A-002 (RI7217 (Fab)), an anti-transferrin receptor antibody.

Briefly, a maleimidocaproyl-L-valine-L-citrulline-p-aminobenzyl alcoholp-nitrophenyl carbonate (MC-Val-Cit-PABC-PNP) linker molecule is coupledto NH2-C6-DUX4 ASO using an amide coupling reaction. Excess linker andorganic solvents are removed by gel permeation chromatography. Thepurified Val-Cit-linker-DUX4 ASO is then coupled to a thiol-reactiveanti-transferrin receptor antibody (DTX-A-002).

The product of the antibody coupling reaction is then subjected tohydrophobic interaction chromatography (HIC-HPLC) to purify themuscle-targeting complex. Densitometry and SDS-PAGE analysis of thepurified complex allow for determination of the average ratio ofASO-to-antibody and total purity, respectively.

Using the same methods as described above, a control complex isgenerated comprising DUX4 ASO covalently linked via a Val-Cit linker toan IgG2a (Fab) antibody.

The purified muscle-targeting complex comprising DTX-A-002 covalentlylinked to DUX4 ASO is then tested for cellular internalization andinhibition of DUX4. Disease-relevant muscle cells that have relativelyhigh expression levels of transferrin receptor, are incubated in thepresence of vehicle control (saline), muscle-targeting complex (100 nM),or control complex (100 nM) for 72 hours. After the 72 hour incubation,the cells are isolated and assayed for expression levels of DUX4.

EQUIVALENTS AND TERMINOLOGY

The disclosure illustratively described herein suitably can be practicedin the absence of any element or elements, limitation or limitationsthat are not specifically disclosed herein. Thus, for example, in eachinstance herein any of the terms “comprising”, “consisting essentiallyof”, and “consisting of” may be replaced with either of the other twoterms. The terms and expressions which have been employed are used asterms of description and not of limitation, and there is no intentionthat in the use of such terms and expressions of excluding anyequivalents of the features shown and described or portions thereof, butit is recognized that various modifications are possible within thescope of the disclosure. Thus, it should be understood that although thepresent disclosure has been specifically disclosed by preferredembodiments, optional features, modification and variation of theconcepts herein disclosed may be resorted to by those skilled in theart, and that such modifications and variations are considered to bewithin the scope of this disclosure.

In addition, where features or aspects of the disclosure are describedin terms of Markush groups or other grouping of alternatives, thoseskilled in the art will recognize that the disclosure is also therebydescribed in terms of any individual member or subgroup of members ofthe Markush group or other group.

It should be appreciated that, in some embodiments, sequences presentedin the sequence listing may be referred to in describing the structureof an oligonucleotide or other nucleic acid. In such embodiments, theactual oligonucleotide or other nucleic acid may have one or morealternative nucleotides (e.g., an RNA counterpart of a DNA nucleotide ora DNA counterpart of an RNA nucleotide) and/or one or more modifiednucleotides and/or one or more modified internucleotide linkages and/orone or more other modification compared with the specified sequencewhile retaining essentially same or similar complementary properties asthe specified sequence.

The use of the terms “a” and “an” and “the” and similar referents in thecontext of describing the invention (especially in the context of thefollowing claims) are to be construed to cover both the singular and theplural, unless otherwise indicated herein or clearly contradicted bycontext. The terms “comprising,” “having,” “including,” and “containing”are to be construed as open-ended terms (i.e., meaning “including, butnot limited to,”) unless otherwise noted. Recitation of ranges of valuesherein are merely intended to serve as a shorthand method of referringindividually to each separate value falling within the range, unlessotherwise indicated herein, and each separate value is incorporated intothe specification as if it were individually recited herein. All methodsdescribed herein can be performed in any suitable order unless otherwiseindicated herein or otherwise clearly contradicted by context. The useof any and all examples, or exemplary language (e.g., “such as”)provided herein, is intended merely to better illuminate the inventionand does not pose a limitation on the scope of the invention unlessotherwise claimed. No language in the specification should be construedas indicating any non-claimed element as essential to the practice ofthe invention.

Embodiments of this invention are described herein. Variations of thoseembodiments may become apparent to those of ordinary skill in the artupon reading the foregoing description.

The inventors expect skilled artisans to employ such variations asappropriate, and the inventors intend for the invention to be practicedotherwise than as specifically described herein. Accordingly, thisinvention includes all modifications and equivalents of the subjectmatter recited in the claims appended hereto as permitted by applicablelaw. Moreover, any combination of the above-described elements in allpossible variations thereof is encompassed by the invention unlessotherwise indicated herein or otherwise clearly contradicted by context.Those skilled in the art will recognize, or be able to ascertain usingno more than routine experimentation, many equivalents to the specificembodiments of the invention described herein. Such equivalents areintended to be encompassed by the following claims.

1.-74. (canceled)
 75. A method of reducing expression level of DUX4 in amuscle cell of a subject, the method comprising administering to thesubject a complex that comprises an anti-transferrin receptor antibodycovalently linked to an oligonucleotide that targets a DUX4 RNA, whereinthe anti-transferrin receptor antibody binds in the range of C89 to F760of human transferrin receptor protein 1 (TfR1) having an amino acidsequence as set forth in SEQ ID NO: 1; wherein the oligonucleotide is asingle stranded oligonucleotide in the range of 15-35 nucleotides inlength, wherein the oligonucleotide comprises a region ofcomplementarity to the nucleotide sequence as set forth in SEQ ID NO:46, wherein the region of complementarity is at least 15 nucleotides inlength, and wherein the oligonucleotide is a phosphorodiamidatemorpholino oligomer; and wherein the complex is administered to thesubject by infusion and the oligonucleotide is configured to bring aboutreduction of expression level of DUX4 in the muscle cell.
 76. The methodof claim 75, wherein the region of complementarity is at least 20nucleotides in length.
 77. The method of claim 75, wherein theoligonucleotide is 100% complementary to the nucleotide sequence of SEQID NO:
 46. 78. The method of claim 75, wherein the oligonucleotidecomprises at least 20 consecutive nucleotides of SEQ ID NO:
 45. 79. Themethod of claim 75, wherein the oligonucleotide comprises the nucleotidesequence of SEQ ID NO:
 45. 80. The method of claim 75, wherein the 5′end of the oligonucleotide is covalently linked to a lysine in theanti-transferrin receptor antibody via a cleavable linker.
 81. Themethod of claim 80, wherein the cleavable linker comprises avaline-citrulline sequence.
 82. The method of claim 80, wherein thecomplex is obtained by a cycloaddition reaction between an azide and analkyne to form a triazole.
 83. The method of claim 82, wherein prior tothe cycloaddition reaction, the azide is located on the cleavable linkerthat is covalently linked to the 5′ end of the oligonucleotide and thealkyne is provided in a bicyclononyne moiety that further covalentlylinks to the anti-transferrin receptor antibody.
 84. The method of claim81, wherein the cleavable linker further comprises one or morepolyethylene glycol units.
 85. The method of claim 75, wherein theanti-transferrin receptor antibody binds to human TfR1 with a K_(D) ofless than 10⁻⁸M.
 86. The method of claim 75, wherein theanti-transferrin receptor antibody is in the form of a ScFv, Fabfragment, Fab′ fragment, F(ab′)2 fragment, or Fv fragment.
 87. Themethod of claim 75, wherein the anti-transferrin receptor antibody is inthe form of a Fab fragment.
 88. The method of claim 75, wherein thesubject has one or more deletions of D4Z4 repeats in chromosome
 4. 89.The method of claim 88, wherein the subject has 10 or fewer D4Z4repeats.
 90. The method of claim 75, wherein the oligonucleotide resultsin reduction of expression levels of one or more of ZSCAN1, MBDL3L2 andTRIM43 in the muscle cell.
 91. The method of claim 75, wherein themuscle cell is a skeletal muscle cell, cardiac muscle cell, or smoothmuscle cell.
 92. The method of claim 75, wherein the subject is human.93. The method of claim 75, wherein the subject is cynomolgus.
 94. Themethod of claim 88, wherein the deletions of D4Z4 repeats in chromosome4 is associated with facioscapulohumeral muscular dystrophy (FSHD). 95.The method of claim 75, wherein the complex is administered to thesubject by intravenous infusion.